BR112021003095A2 - methods related to bronchial premalignant lesion severity and progression - Google Patents

Abstract

METHODS RELATED TO THE SEVERITY AND PROGRESSION OF PRE-MALIGNANT BRONCHIAL INJURY. The technology described in this application is directed to methods of treating and diagnosing premalignant bronchial lesions, for example, by determining the lesion subtype using one or more biomarkers described herein.

Description

“METHODS RELATED TO THE SEVERITY AND PROGRESSION OF PRE-MALIGNANT BRONCHIAL INJURY”. REFERENCE TO RELATED REQUESTS

[0001] This application claims benefit under 35 U.S.C. § 119(e) of US Interim Application No. 62/765,264, filed August 20, 2018, the contents of which are incorporated herein by reference in its entirety.

GOVERNMENT SUPPORT

[0002] The present invention was made with Government support under contract No. CA196408, granted by the National Institutes of Health. The Government has certain rights in the invention.

TECHNICAL FIELD

[0003] The technology described in the present application relates to the treatment, diagnosis and monitoring of treatment for bronchial premalignant lesions.

BACKGROUND

[0004] Squamous cell lung cancer develops from non-cancerous lesions in the airways known as pre-malignant bronchial lesions. The presence of persistent or progressive dysplastic premalignant bronchial lesions is a marker of increased risk of lung cancer, both at the site of the lesion (where they are the presumed precursors of squamous cell lung cancer) and elsewhere in the lung. Not all premalignant bronchial lesions progress to invasive cancer, and those that do progress at variable rates with variable outcomes. There are currently no tools available in the clinic to identify which lesions will progress to cancer and which will not. In addition, the current technology for detecting premalignant bronchial lesions is through autofluorescence and white light bronchoscopy. A bronchoscopy procedure is invasive and is only moderately sensitive and specific in detecting small premalignant bronchial lesions, as it requires visualization of the lesions. Finally, to date, the only treatment for premalignant bronchial lesions is removal of the lesions through surgery or bronchoscopy.

SUMMARY

[0005] The inventors have now developed: 1) tests for the presence of pre-malignant bronchial lesions (some of which do not require bronchoscopy and use the surprising finding that normal tissues in other parts of the airway exhibit biomarkers that indicate the presence of lesions bronchial premalignant lesions in the individual), 2) methods to determine whether bronchial premalignant lesions are likely to progress to cancer, 3) novel therapies for bronchial premalignant lesions that target the underlying molecular changes that characterize premalignant lesions. -bronchial malignancies.

[0006] Consequently, an aspect provided herein is a method of treating premalignant bronchial lesions, the method comprising: administering at least one of: (i) a bronchoscopy-based procedure to examine the central airway and a chest computed tomography; (ii) at least every 6 months, one of a bronchoscopy-based procedure to examine the central airway and a chest CT scan; and/or (iii) at least one anti-proliferative drug; to an individual determined to have at least one of: (a) an increased expression level of at least one module 5 gene compared to a reference level of non-proliferative lesion; and (b) a reduced expression level of at least one module 6 gene compared to a reference level of non-proliferative lesion.

[0007] In one embodiment of this and all other aspects provided herein, at least one of the module 5 gene is selected from the group consisting of: RACGAP1 and TPX2; and at least one of the module 6 gene is selected from the group consisting of: NEK11 and IFT88.

[0008] In another embodiment of this and all other aspects provided herein, the individual is further determined to have an increased expression level of at least one module 7 or module 4 gene.

[0009] In another embodiment of this and all other aspects provided herein, at least one of the module 7 or module 4 gene is selected from the group consisting of: COX6A1; COX7A2; RPL26; and RPL23.

[0010] In another embodiment of this and all other aspects provided herein, the expression level of each of the genes in Table 15 is determined.

The method according to any one of claims 1 to 5, is characterized in that at least one of the antiproliferative drug is selected from the group consisting of: Acetylcholine receptor antagonist; Acetylcholinesterase inhibitors; Adenosine receptor antagonists; Adrenergic receptor antagonists; AKT Inhibitors; Angiotensin receptor antagonists; Apoptosis stimulants; Aurora kinase inhibitors; CDK Inhibitors; Cyclooxygenase inhibitors; Inhibitors of cytokine production; Dehydrogenase Inhibitors; DNA protein kinase inhibitors; Focal adhesion inhibitors; Dopamine receptor antagonists; EGFR Inhibitors; ERK1 and ERK2 phosphorylation inhibitors; Estrogen receptor agonists; EZH2 Inhibitors; FLT3 Inhibitors; Glucocorticoid receptor agonists; Glutamate receptor antagonists; HDAC inhibitors; Histamine Receptor Antagonists; Histone Lysine Methyltransferase Inhibitors; HSP Inhibitors; IKK inhibitors; Ion channel antagonists; JAK inhibitors; JNK inhibitors; KIT inhibitors; Leucine-rich repeat kinase inhibitors; MDM Inhibitors; mediator release inhibitors; MEK Inhibitors; MTOR inhibitors; Monoamine oxidase inhibitors; NFB pathway inhibitors; Nucleophosmin Inhibitors; PARP inhibitors; PPAR receptor agonists; PI3K inhibitors; Tyrosine kinase inhibitors; Phosphodiesterase Inhibitors; Protein kinase inhibitors; RAF inhibitors; RNA polymerase inhibitors; topoisomerase inhibitors; RNA synthesis inhibitors; SIRT Inhibitors; Sodium channel blockers; VEGFR Inhibitors; and Vitamin D receptor agonists.

[0011] In another embodiment of this and all other aspects provided herein, the antiproliferative drug is administered as an inhaled formulation or topical formulation.

[0012] In another embodiment of this and all other aspects provided herein, the antiproliferative drug is administered during a bronchoscopy-based procedure.

[0013] In another embodiment of this and all other aspects provided herein, the antiproliferative drug is administered systemically.

[0014] In another embodiment of this and all other aspects provided herein, the antiproliferative drug is administered during a bronchoscopy-based procedure and systemically.

[0015] Another aspect provided herein relates to a method of treating bronchial premalignant lesions, the method comprising: administering at least one of: (i) a bronchoscopy-based procedure to examine the central airway and a chest computed tomography; (ii) at least every 6 months, one of a bronchoscopy-based procedure to examine the central airway and a chest CT scan; and/or (iii) at least one anti-proliferative drug; to an individual determined to have at least one of: (a) an increased expression level of at least one module 5 gene compared to a reference level of non-proliferative lesion; and (b) a reduced expression level of at least one module 6 gene compared to a non-proliferative lesion reference level, wherein the individual is further determined to have a reduced expression level of at least one module 9 gene. compared to a reference level of non-proliferative lesion and/or an increased expression level of at least one gene from module 10 compared to a reference level of non-proliferative lesion.

[0016] In one embodiment of this and all other aspects provided herein, the individual is determined to have a reduced expression level of at least one module 9 gene and/or an increased expression level of at least one module gene. module 10 receives at least one of: i. either a bronchoscopy-based procedure to examine the central airway in which lesions are biopsied to remove abnormal tissue, and a CT scan of the chest; ii. at least every 6 months, one of a bronchoscopy-based procedure to examine the central airway, in which lesions undergo biopsy to remove abnormal tissue and a CT scan of the chest; and/or iii. at least one immunostimulating drug.

[0017] Also provided herein, in another aspect, is a method of treating bronchial premalignant lesions, the method comprising: administering at least one of: (i) both a bronchoscopy-based procedure to examine the airway central, in which lesions undergo biopsy to remove abnormal tissue, such as a chest CT scan; (ii) at least every 6 months, one of a bronchoscopy-based procedure to examine the central airway, in which lesions undergo biopsy to remove abnormal tissue and a CT scan of the chest; and/or (iii) at least one immunostimulating drug; to an individual determined to have a reduced expression level of at least one module 9 gene compared to a non-proliferative lesion reference level and/or an increased expression level of at least one module 10 gene compared to a level of reference of non-proliferative lesion.

[0018] In an embodiment of this and all other aspects provided herein, the module 9 gene is selected from the group consisting of: EPSTI1; UBE2L6; B2M and TAP1.

[0019] In another embodiment of this and all other aspects provided herein, at least one of the module 9 gene is selected from Table 16.

[0020] In another embodiment of this and all other aspects provided in this document, the module gene

10 is selected from the group consisting of: CACNB3 and MAPK10.

[0021] In another embodiment of this and all other aspects provided herein, at least one of the immunostimulating drug is selected from the group consisting of: Immune checkpoint inhibitors (e.g., inhibitors against PD-1, PD-L1, CTLA4, and LAG3); Drugs that stimulate interferon signaling (eg, antiviral drugs that improve interferon signaling); DNA synthesis inhibitors; IMDH inhibitors; CDK Inhibitors; Ribonucleotide reductase inhibitors; Dihydrofolate reductase inhibitors; topoisomerase inhibitors; FLT3 Inhibitors; IGF-1 Inhibitors; MEK Inhibitors; Aurora kinase inhibitors; PKC Inhibitors; RAF inhibitors; PDFGR/KIT inhibitors; VEGFR Inhibitors; SRC inhibitors; Retinoid receptor agonists; HDAC inhibitors; DNA methyltransferase inhibitors; and EZH2 Inhibitors.

[0022] Another aspect provided herein relates to a method of treating bronchial premalignant lesions, the method comprising: administering at least one of: (i) a bronchoscopy-based procedure to examine the central airway and a chest computed tomography; (ii) at least every 6 months, one of a bronchoscopy-based procedure to examine the central airway and a chest CT scan; and/or (iii) at least one anti-inflammatory drug; to an individual determined to have at least one of: (a) an increased expression level of at least one module 2 gene compared to a non-inflammatory reference level; and (b) a reduced expression level of at least one module 6 gene compared to a non-inflammatory reference level.

[0023] In one embodiment of this aspect and all other aspects provided herein, at least one of the module 2 gene is selected from the group consisting of: MSANTD2, CCNL2 and LUC7L; and at least one of the module 6 gene is selected from the group consisting of: NEK11 and IFT88.

[0024] In another embodiment of this and all other aspects provided herein, the individual is further determined to have an increased expression level of at least one module 7 gene, module 1 gene or module 8 gene and/ or reduced expression level of at least one module 4 gene or one module 5 gene.

[0025] In another embodiment of this and all other aspects provided herein, at least one of the module 7 gene is selected from the group consisting of: RPL26 and RPL23.

[0026] In another embodiment of this and all other aspects provided herein, at least one of the module 1 gene is selected from the group consisting of: KIRREL; PHLDB1; and MARVELD1.

[0027] In another embodiment of this and all other aspects provided herein, at least one of the module 8 gene is selected from the group consisting of: DOC2; CD53; and LAPTM.

[0028] In another embodiment of this and all other aspects provided herein, at least one of the module 4 gene is selected from the group consisting of: COX6A1 and COX7A2.

[0029] In another embodiment of this and all other aspects provided herein, at least one of the module 5 gene is selected from the group consisting of: RACGAP1 and TPX2.

[0030] In another embodiment of this and all other aspects provided in this document, the expression level of each of the genes in Table 15 is determined.

[0031] In another embodiment of this and all other aspects provided herein, at least one of the anti-inflammatory drug is selected from the group consisting of: Acetylcholine receptor antagonists;

Acetylcholinesterase inhibitors; Adenosine receptor antagonists; Adrenergic receptor antagonists;

Angiotensin receptor antagonists; Antibodies

IL1B; Apoptosis stimulants; Kinase Inhibitors

Aurora; CDK Inhibitors; Cyclooxygenase inhibitors;

Inhibitors of cytokine production; Dehydrogenase Inhibitors; Dopamine receptor antagonists;

EGFR Inhibitors; ERK1 and ERK2 phosphorylation inhibitors;

Estrogen receptor agonists; FLT3 Inhibitors;

Glucocorticoid receptor agonists; Glutamate receptor antagonists; HDAC inhibitors; Histamine Receptor Antagonists; Histone Lysine Methyltransferase Inhibitors; HSP Inhibitors; IKK inhibitors;

Ion channel antagonists; KIT inhibitors; Leucine-rich repeat kinase inhibitors; MEK Inhibitors;

MDM Inhibitors; Phosphodiesterase Inhibitors; Monoamine oxidase inhibitors; MTOR inhibitors; NFB pathway inhibitors; Nucleophosmin Inhibitors; PARP inhibitors;

PI3K inhibitors; PPAR receptor agonists; Protein synthesis inhibitors (eg chloramphenicol);

RAF inhibitors; SIRT Inhibitors; Sodium channel blockers; TGF beta receptor inhibitors;

topoisomerase inhibitors; Tyrosine kinase inhibitors; VEGFR Inhibitors; and Vitamin D receptor agonists.

[0032] In another embodiment of this and all other aspects provided herein, the anti-inflammatory drug is administered during a bronchoscopy-based procedure.

[0033] In another embodiment of this and all other aspects provided herein, the anti-inflammatory drug is administered systemically.

[0034] In another embodiment of this and all other aspects provided herein, the anti-inflammatory drug is administered during a bronchoscopy-based procedure and systemically.

[0035] In another embodiment of this and all other aspects provided herein, at least one of the gene is selected from Table 14.

[0036] In another embodiment of this and all other aspects provided in this document, the expression level of each of the genes in Table 14 is determined.

[0037] In another embodiment of this and all other aspects provided herein, the development of lung cancer or squamous cell carcinoma of the lung is prevented, delayed or reduced.

[0038] In another embodiment of this and all other aspects provided herein, lung cancer is squamous cell carcinoma of the lung.

[0039] In another embodiment of this and all other aspects provided herein, the expression level is the level of expression in an endobronchial biopsy, endobronchial smear sample, upper airway biopsy, upper airway smear sample , nasal epithelial cells, sputum, or blood obtained from the individual.

[0040] In another embodiment of this and all other aspects provided herein, the expression level is the level of expression in a bronchial smear taken from the right or left main bronchus.

[0041] In another embodiment of this and all other aspects provided herein, the biopsy sample or smear comprises morphologically normal tissues or cells.

[0042] In another embodiment of this and all other aspects provided herein, the biopsy or smear sample consists of morphologically normal cells or tissues.

[0043] In another embodiment of this and all other aspects provided herein, the expression level is the expression level in a sample comprising premalignant bronchial lesion cells.

[0044] In another embodiment of this and all other aspects provided herein, the expression level is the level of expression in a sample comprising morphologically normal cells.

[0045] In another embodiment of this and all other aspects provided herein, the individual is a smoker or ex-smoker.

BRIEF DESCRIPTION OF THE DRAWINGS

Figures 1A-1E demonstrate that endobronchial biopsies divide into four distinct molecular subtypes that correlate with clinical and molecular phenotypes. (Figure 1A) Genes (n = 3936) organized into 9 gene coexpression modules were used to discover four molecular subtypes (Proliferative, Inflammatory, Secretory and Normal) in the 190 DC biopsies using consensus clustering. The thermal map shows semi-supervised hierarchical clustering of normalized gene expression with z-scores between 3,936 genes and 190 DC biopsies. The top bar represents the four molecular subtypes: Proliferative (n = 52 samples), Inflammatory (n = 37 samples), Secretor (n = 61 samples), and Normal (n = 40 samples). Throughout the figures, the four subtypes of molecules are represented by four shades of gray, increasing the luminosity in relation to the order given in the previous sentence. On the left side of the heat map, the average of the first major component calculated across the module genes is plotted for each subtype. On the right side of the heat map, a summary of the enriched biological pathways is listed for each module. (Figure 1B) Blister plots showing significant associations (p < 0.01 by Fisher's Exact Test) between molecular subtypes and smoking, histological grade of biopsy, and predicted LUSC tumor molecular subtypes. The columns represent the 4 molecular subtypes (Proliferative, Inflammatory, Secretory and Normal) and the diameter of the circle is proportional to the number of samples within each subtype that have the phenotype in the row. (Figure 1C) Box diagram of MKI67 expression values in biopsies with normal histology or hyperplasia (n = 8, 16, 26, 18 in Proliferative, Inflammatory, Secretory, and Normal subtypes, respectively). Proliferative subtype MKI67 expression levels are significantly higher than Non-Proliferative subtype samples (FDR = 3.4e-10).

(Figure 1D) Box diagram of MKI67 expression values in biopsies with dysplastic histology (n = 33, 11, 19, 9 in the Proliferative, Inflammatory, Secretory and Normal subtypes, respectively). Proliferative subtype MKI67 expression levels are significantly higher than Non-Proliferative subtype samples (FDR = 3.1e-8).

(Figure 1E) Immunofluorescent staining demonstrating increased staining of MKI67 and KRT5 and reduced staining of TUB1A1 in the Proliferative subtype in agreement with the expression of the corresponding marker genes. Representative samples shown for the Proliferative and Inflammatory subtypes have dysplasia histology, while the samples shown for the Secretor and Normal subtypes have normal histology (magnification 200X).

[0047] Figures 2A-2D demonstrate that phenotypic associations with molecular subtypes are confirmed in an independent set of samples. (Figure 2A) The 190 DC biopsies and the 3,936 genes were used to construct a closer centroid molecular subtype classifier of 22 genes. Semi-supervised hierarchical clustering of normalized gene expression with z-scores among 22 classifier genes and 190 training samples of DC biopsies. (Figure 2B) The closest centroid molecular subtype classifier of 22 genes was used to predict the molecular subtypes of the 105 VC biopsies. The semi-supervised hierarchical cluster of normalized gene expression with z-scores in 22 genes and 105 CV is represented. The heat map lines provide the gene name and module association, and the column color bar shows the molecular subtype association. (Figure 2C) Blister plots showing significant associations (p < 0.01 by Fisher's Exact Test) between VC molecular subtypes and smoking status, biopsy histological grade, and predicted LUSC tumor molecular subtypes. The columns represent the 4 molecular subtypes (Proliferative, Inflammatory, Secretory and Normal) and the radius of the circle is proportional to the number of samples within each subtype that have the phenotype in the row. (Figure 2D) Blister plots showing significant associations (p < 0.01 by Fisher's Exact Test) between VC molecular subtypes and smoking status, biopsy histological grade, and predicted LUSC tumor molecular subtypes. The columns represent the 4 molecular subtypes (Proliferative, Inflammatory, Secretory and Normal) and the radius of the circle is proportional to the number of samples within each subtype that have the phenotype in the row.

Figures 3A-3C demonstrate the performance of the molecular subtype classifier on upper airway smears of normal-appearing epithelium collected at the same time as endobronchial biopsies. (Figure 3A) The DC (left) and VC (right) cohorts, showing the number of smears (y-axis) predicted to be positive for the Proliferative subtype that have at least one biopsy (y-axis) with a Proliferative subtype classification at the time where the smear was collected. (Figure 3B) Box diagram of PC1 for Modules 4, 5, 6, and 7 (y-axis) across the four molecular subtypes for each cohort (x-axis).

The asterisk indicates significant differences between the Proliferative subtype versus all other samples (FDR < 0.05).

(Figure 3C) Box diagram of PC1 for Modules 4, 5, 6, and 7 (y-axis) across the four molecular subtypes for each cohort (x-axis). The asterisk indicates significant differences between the Proliferative subtype versus all other samples (FDR < 0.05).

Figures 4A-4H demonstrate that the enriched module for interferon signaling and antigen processing is associated with progression/persistence on biopsy and a depletion of innate and adaptive immune cells in the Proliferative subtype. (Figures 4A and 4F) Module 9 gene metagene expression among DC biopsies within the Proliferative subtype (p = 0.002 between progressive/persistent versus regressive biopsies). Biopsy progression/regression was defined for each biopsy based on the histology of the biopsy and the worst histology recorded for the same lung anatomical location in the future. Histological changes between normal,

hyperplasia and metaplasia were classified as "normal stable", decreases in the grade of histological dysplasia or changes from dysplastic histology to normal/hyperplasia/metaplasia were classified as

"regressive", the lack of future histological data was classified as "unknown" and everything else was classified as "progressive/persistent". (Figures 4B and

4G) Box diagram of the percentages of positively stained cells for CD68 and CD163, CD68, CD163, CD4 and

CD8 between progressive/persistent and regressive biopsies

(p < 0.001 for all comparisons). The x-axis labels indicate the number of regions (R) enumerated among individuals (P) for each coloration and result group represented in the box diagram.

Biopsies were included in the analysis if their clinical results were in agreement with the score for Module 9. (Figure 4B)

Metagene expression of Module 9 genes among VC biopsies within the Proliferative subtype (p = 0.03 between progressive/persistent versus regressive biopsies). (Figure 4C)

Above: Normalized gene expression with Z scores on 112 genes in Module 9, DC biopsies (left) and VC biopsies (right). Each thermal map is monitored according to the GSVA scores from Module 9. The upper bars indicate the histological grade of the biopsies and their progressing status. Below: xCell results indicating the relative abundance of immune cell types in DC biopsies (left) and VC biopsies (right). The displayed immune cell types are significantly associated with lesion progression/persistence (FDR < 0.05 in both CD and VC after adjusting for differences in epithelial cell content). (Figure 4D) Representative histology in which the dashed line denoted the separation of epithelium and stromal compartment. Upper panels: a severe progressive dysplasia reduced the presence of immune cells demonstrated by the marked reduction in the expression of M2 macrophages (CD68/163 staining, double positive cells indicated by arrows) and CD8 T cells. (Sample corresponds to *P in Figure 4C.) Lower panels: A moderately regressive dysplasia increased the presence of immune cells, including M2 macrophages (CD68/163 double positive cell staining indicated by arrows) and CD8 T cells.

(Samples correspond to *P in Figure 4C.) (Figures 4E and 4H) Box diagram of the percentages of cells stained positively for CD68 and CD163, CD68, CD163, CD4 and CD8 between progressive/persistent and regressive biopsies (p < 0.001 for all comparisons). The x-axis labels indicate the number of regions (R) enumerated among individuals (P) for each coloration and the group of results represented in the box diagram. Biopsies were included in the analysis if their clinical results were in agreement with the score for Module 9.

[0050] Figure 5 represents Batch Information and Alignment Statistics in Samples in both the Discovery and Validation cohorts. Statistical tests between Discovery and Validation cohorts were performed using Fisher's exact test for categorical variables and Student's t test for continuous variables. Percentages are reported for categorical variables and mean and standard deviations are reported for continuous variables.

[0051] Figure 6 represents a summary of the Genetic Modules. The module number, number of genes in the module, biological pathways and selected genes associated with the module and an FDR value for the difference in GSVA scores for the module between the molecular subtypes are reported.

[0052] Figure 7 represents a list of samples used for immunofluorescence studies.

[0053] Figure 8 represents the distribution of molecular subtypes by individual. The columns represent the 4 molecular subtypes (Proliferative, Inflammatory, Secretory and Normal) and the radius of the circle is proportional to the number of samples within each subtype.

[0054] Figure 9 represents a graph of Proliferation Quantification by Immunofluorescent Staining, Basal Cell Markers and Hair Cells Among Molecular Subtypes. Box diagram of the quantification of immunofluorescent staining of KI67 (proliferation), KRT5 (basal cells) and TUB1A1 (hair cells) in representative samples of each molecular subtype (Proliferative n = 4, Inflammatory n = 3, Secretor n = 1, Normal n = 1). KI67 and KRT5 staining is significantly higher in samples in the Proliferative subtype (p = 0.02 and p = 0.01, respectively, for sample differences between the Proliferative subtype and other subtypes). TUB1A1 was lower in samples in the Proliferative and Inflammatory subtypes, but did not reach statistical significance (p = 0.07 for sample differences between the Proliferative and Inflammatory subtypes versus the Inflammatory and Secretory subtypes).

[0055] Figures 10A-10H represent box diagrams of deconvolution results for selected genes and cell types in the Discovery and Validation cohorts by molecular subtype. (Figures 10A-10D) Biopsies from the Discovery cohort. (Figures 10E-10H) Validation cohort biopsies. (Figure 10A) and (Figure 10E) show box diagrams of gene expression levels of trigger genes in

LUSC identified by TCGA in the molecular subtypes.

(Figure 10B) and (Figure 10F) show box diagrams of gene expression levels of cell-type marker genes across molecular subtypes. (Figure 10C) and (Figure 10G) show box diagrams of GSVA scores calculated using gene sets from Dvorak et al. through molecular subtypes. (Figure 10D) and (Figure 10H) show box diagrams of ESTIMATE scores across molecular subtypes. The ESTIMATE algorithm estimates the stromal (StromalScore), immune (ImmunScore) and epithelial (ESTIMATScore) cell fractions in each sample.

High immune and stromal scores indicate a high fraction of stromal and immune cells, while low epithelial scores indicate a high fraction of epithelial cells.

[0056] Figure 11 represents a thermal map of the Molecular Subtype Classifier of 22 genes in the Discovery and Validation Cohort Biopsies. Semi-supervised hierarchical grouping of the z-score normalized residual gene expression between the 22 classifier genes and 190 training samples of DC biopsies (left) and 105 VC biopsies (right). The lines on the thermal map show the association of the gene module. The first color bar in the column shows the molecular subtype association in the

CD and the predicted subtype association for 22 genes in CV.

The second color bar in the column represents correct and incorrect predictions in CD using the 22 gene classifier and molecular subtypes derived by performing consensus clustering across the CV.

[0057] Figure 12 represents graphs of the behavior of the gene module through the molecular subtypes in the biopsies of the Discovery and Validation cohorts. The average of the first major component calculated among the genes in the module is plotted for each molecular subtype.

[0058] Figure 13 represents the agreement between Module 9 and two cell type deconvolution analyses.

Top: Hierarchical clustering of normalized gene expression with z-scores on 112 genes in module 9, DC biopsies (left) and VC biopsies (right). Each thermal map is monitored according to the GSVA scores from module 9. The upper bars indicate the histological grade of the biopsies and their progressing status.

xCell results (medium) and GSVA scores for gene sets described by Bindea et al. (bottom) indicating the relative abundance of immune cell types in DC biopsies (left) and VC biopsies (right). The displayed immune cell types are significantly associated with lesion progression/persistence (FDR < 0.05 in DC and VC).

[0059] Figure 14 represents a tracheobronchial map of the locations of the sites collected through endobronchial biopsy.

[0060] Figure 15 represents the distribution of individuals among the endobronchial biopsies of the Discovery cohort among the four molecular subtypes. Genes (n =

3936) arranged in 9 gene coexpression modules were used to discover four molecular subtypes (Proliferative, Inflammatory, Secretory and Normal) across the 190 Discovery cohort (DC) biopsies using consensus clustering. The thermal map shows semi-supervised hierarchical clustering of normalized gene expression with z-scores between 3,936 genes and 190 DC biopsies. The upper color bars represent the individual from which the sample was derived and the members of the molecular subtype: Proliferative (n = 52 samples), Inflammatory (n = 37 samples), Secretor (n = 61 samples) and Normal (n = 40 samples). On the left side of the heat map, the average GSVA module score for each subtype is represented.

[0061] Figure 16 represents the distribution of the molecular subtype for each individual throughout the bronchoscopy procedures. The bar graph shows, for each individual and each bronchoscopy procedure, the number of biopsies collected and their corresponding molecular subtype. The y axis indicates the subject's number and whether or not that subject had a prior history of squamous cell carcinoma of the lung (LUSC) or another type of lung cancer (Other). The Discovery cohort includes individuals 1 to 32 and the Validation cohort includes individuals 33 to 52. No difference was detected in the diversity of subtype classifications within an individual based on prior history of lung cancer (Shannon mean entropy of subtype classifications in patients with a history of lung cancer = 1.12, n = 32 vs. patients without a history of lung cancer = 1.25, n = 17; p-value by Wilcoxon Rank Sum test = 0. 43).

DETAILED DESCRIPTION

As described herein, it has been found that premalignant lesions in an individual's airways can be characterized as being one of five types: normal, secretory, inflammatory, progressive proliferative, and persistent proliferative. Identifying premalignant lesions as one of these types allows for more effective treatment of the individual, as different types of lesions respond to different treatments and require different treatments and monitoring regimens.

Consequently, methods of treatment related to the treatment of premalignant bronchial lesions in an individual are provided herein. Such methods may comprise testing, testing and/or identifying the type of injury and administering appropriate therapeutic regimens for that type of injury.

[0063] As used herein, "premalignant lesion" refers to an epithelial lesion or dysplasia that is a precursor or may be a precursor of cancer. The basement membrane is intact, with no possibility of metastatic spread, unlike cancer. A premalignant bronchial lesion is a premalignant lesion present in the bronchial epithelium of an individual. Bronchial premalignant lesions are usually small and may be difficult to visualize using conventional white light bronchoscopy.

Bronchial premalignant lesions may exhibit one of the five phenotypes described herein, particularly progressive proliferative, persistent proliferative, secretory, inflammatory, and normal. The subtype names refer to major differences in the activity of the molecular pathway that differentiates the subtypes from one another. The different lesion phenotypes can be distinguished from each other and from normal tissue by using the gene expression patterns described in this document.

As explained in detail elsewhere in this document, the gene expression patterns identified here refer to 10 gene modules, where each module is a group of genes with similar expression patterns across different subtypes of bronchial premalignant lesions. The identity of each of the modules, for example the genes that comprise each module, is provided in Table 13 herein. Briefly, proliferative lesions (progressive and persistent) are distinguished by having an increased expression of modules 4, 5 and 7 and a decreased expression of module 6. Progressive proliferative lesions can be distinguished from persistent proliferative lesions by the fact that they have a decrease in modulo 9 expression and/or an increase in modulo 10 expression. Secretory lesions are distinguished by an increase in modulo 6 expression and a decrease in modulo 1 expression and, optionally, an increase in modulo 8 expression and a decrease in expression of modulo 2, 5 and 7. The Normal type is distinguished by an increase in expression in modulo 6 and a decrease in expression in modulo 9 and, optionally, an increase in expression in modulo 1 and a decrease in expression in modulo 8.

[0065] Standard treatment for individuals at risk for lung cancer, or who have been identified with pre-existing lesions.

bronchial malignancies, is the annual screening for lung cancer

(eg, a bronchoscopy and/or computed tomography of the chest). When an individual has a premalignant proliferative bronchial lesion, such treatment is no longer sufficient and the individual must be treated more aggressively.

Accordingly, in one aspect of any of the modalities, a method of treating bronchial premalignant lesions is provided herein, the method comprising administering at least one of: i) a bronchoscopy-based procedure to examine the central airway and a chest computed tomography; ii)

at least every 6 months, at least one of a bronchoscopy-based procedure to examine the central airway and a chest CT scan; and/or iii) at least one anti-proliferative drug to a subject determined to have at least one of a) an increased expression level of at least one module 5 gene compared to a reference level; and b) a reduced expression level of at least one module 6 gene compared to a reference level.

In one aspect of either embodiment, a method of treating bronchial premalignant lesions is provided herein, the method comprising determining an individual to have at least one of a) an increased expression level of at least one gene of the module 5 compared to a reference level; and b) a reduced expression level of at least one module 6 gene compared to a reference level and administering at least one of: i) a bronchoscopy-based procedure to examine the central airway and a computed tomography scan of the chest; ii) at least every 6 months (eg at least every 1, 2, 3, 4, 5 or 6 months), at least one of a bronchoscopy-based procedure to examine the central airway and a CT scan chest; and/or iii) at least one anti-proliferative drug to the subject. In some modalities of either aspect, the reference level is a non-proliferative reference level.

[0066] In some embodiments, if the individual is determined not to have at least one of a) an increased expression level of at least one module 5 gene compared to a reference level; and b) a reduced expression level of at least one module 6 gene compared to a reference level, the subject does not receive an antiproliferative drug and receives a bronchoscopy-based procedure to examine the central airway and/or a CT scan of the chest no more often than every 6 months (eg, no more often than every 6, 7, 8, 9, 10, 11, or 12 months).

In some embodiments, the individual is determined to lack a) a high level of expression of at least one module 5 gene compared to a reference level; and b) a reduced expression level of at least one module 6 gene compared to a reference level, the subject does not receive an antiproliferative drug and receives a bronchoscopy-based procedure to examine the central airway and/or a CT scan of the chest no more often than every 6 months (eg, no more often than every 6, 7, 8, 9, 10, 11, or 12 months).

[0067] The gene expression of modules 5 and 6, in a bronchial smear sample, is sufficient to identify an individual who has a Proliferative subtype lesion. This avoids the need to visualize and/or collect the actual lesion. Accordingly, in one aspect of any of the modalities, a method of treating bronchial premalignant lesions is provided herein, the method comprising administering at least one of: i) a bronchoscopy-based procedure to examine the central airway and a chest computed tomography; ii) at least every 6 months, at least one of a bronchoscopy-based procedure to examine the central airway and a chest CT scan;

and/or iii) at least one anti-proliferative drug for a subject determined to have, in a bronchial smear sample, a) an increased expression level of at least one module 5 gene compared to a reference level; and b) a reduced expression level of at least one module 6 gene compared to a reference level.

In one aspect of either embodiment, a method of treating bronchial premalignant lesions is provided herein, the method comprising determining an individual as having, in a bronchial smear sample obtained from the individual, a) a level of expression increased by at least one module 5 gene compared to a reference level; and b) a reduced expression level of at least one module 6 gene compared to a reference level and administering at least one of: i) a bronchoscopy-based procedure to examine the central airway and a computed tomography scan of the chest; ii) at least every 6 months,

at least one of a bronchoscopy-based procedure to examine the central airway and a chest CT scan; and/or iii) at least one anti-proliferative drug to the subject.

In some modalities of either aspect, the reference level is a non-proliferative reference level. In some modalities of either aspect, the bronchial smear is taken from a morphologically normal location in the right or left main bronchus. In some modalities of either aspect, the bronchial smear is taken from a visually normal location in the right or left main bronchus.

The module 5 and module 6 genes are provided in Table 13. At least one of the module 5 gene and/or module 6 gene can be any one or more of the module 5 and 6 genes listed in Table 13.

[0069] In some embodiments of either aspect, the expression level of at least one gene from module 5 or at least one gene from module 6 is determined. In some embodiments of either aspect, the level of expression is determined of two or more module 5 genes or two or more module 6 genes. In some embodiments of either aspect, the expression level of each module 5 gene or each module 6 gene of Table 13 is determined.

[0070] In some embodiments of any aspect, the expression level of at least one gene from module 5 and at least one gene from module 6 is determined. In some embodiments of either aspect, the level of expression is determined of two or more module 5 genes and two or more module 6 genes. In some embodiments of either aspect, the expression level of each module 5 gene and each module 6 gene of Table 13 is determined.

[0071] In some embodiments of either aspect, at least one of the module 5 gene comprises either RACGAP1 or TPX2. In some embodiments of either aspect, at least one of the module 5 gene comprises or is RACGAP1 and TPX2. In some embodiments of either aspect, at least one of the module 6 gene comprises or is NEK11 or IFT88. In some embodiments of either aspect, at least one of the module 6 gene comprises or is NEK11 and IFT88.

[0072] The Proliferative subtype is further distinguished by increased expression of module 7 and/or 4. Consequently, in some modalities of either aspect, the individual is further determined to have an increased expression level of at least one gene of the modulo 7 or modulo 4 compared to a reference level. In some embodiments of either aspect, the individual is further determined to have an increased expression level of at least one module 7 gene and at least one module 4 gene compared to a reference level. In some modalities of either aspect, the reference level is a non-proliferative reference level.

[0073] The module 4 and 7 genes are provided in Table 13. At least one of the module 4 gene and/or module 7 gene can be any one or more of the modules 4 and 7 genes listed in Table 13.

[0074] In some embodiments of either aspect, the expression level of at least one module 4 gene or at least one module 7 gene is determined. In some embodiments of either aspect, the expression level is determined of two or more genes from module 4 or two or more genes from module 7. In some embodiments of either aspect, the expression level of each module 4 gene or each module 7 gene of Table 13 is determined.

[0075] In some embodiments of either aspect, the expression level of at least one module 4 gene and at least one module 7 gene is determined. In some embodiments of either aspect, the expression level of two or more module 4 genes and two or more module 7 genes is determined. In some embodiments of either aspect, the expression level of each module 4 gene and each module 7 gene of Table 13 is determined.

[0076] In some embodiments of either aspect, at least one of the module 4 gene comprises either COX6A1 or COX7A2. In some embodiments of either aspect, at least one of the module 4 gene comprises or is COX6A1 and COX7A2. In some embodiments of either aspect, at least one of the module 7 gene comprises or is RPL26 or RPL23. In some embodiments of either aspect, at least one of the module 7 gene comprises or is RPL26 and RPL23.

[0077] When the individual presents with progressive premalignant proliferative bronchial lesion, aggressive treatment may be indicated, even beyond what is foreseen for the premalignant proliferative bronchial lesion. Accordingly, in one aspect of any of the modalities, a method of treating bronchial premalignant lesions is provided herein, the method comprising administering at least one of: i) a bronchoscopy-based procedure to examine the central airway and a chest computed tomography; ii) at least every 6 months, at least one of a bronchoscopy-based procedure to examine the central airway and a chest CT scan; iii) at least one immunostimulating drug and/or iv) at least one immunostimulating drug and at least one antiproliferative drug to an individual determined to have a reduced expression level of at least one module 9 gene compared to a reference level and/ or an increased expression level of at least one module 10 gene compared to a reference level.

In one aspect of either mode,

a method of treating bronchial premalignant lesions is provided herein, the method comprising a)

determining an individual to have a reduced expression level of at least one module 9 gene compared to a reference level and/or an increased expression level of at least one module 10 gene compared to a reference level and b) administer by minus one of: i) a bronchoscopy-based procedure to examine the central airway and a chest CT scan; ii)

at least every 6 months, at least one of a bronchoscopy-based procedure to examine the central airway and a chest CT scan; iii) at least one immunostimulating drug and/or iv) at least one immunostimulating drug and at least one drug antiproliferative to the subject.

In some modalities of either aspect, the reference level is a non-proliferative reference level.

In some embodiments of either aspect, the bronchoscopy-based procedure further comprises biopsy of the lesions to remove the abnormal tissue.

[0078] In some embodiments, if the individual is determined not to have a reduced expression level of at least one module 9 gene compared to a reference level and/or not to have an increased expression level of at least one modulo gene module 10 compared to a reference level, the individual i) does not receive an immunostimulating drug, ii) does not receive an immunostimulating drug and an antiproliferative drug, iii) receives a procedure based on bronchoscopy and/or a CT scan of the chest no more often than every 6 months (eg, no more often than every 6, 7, 8, 9, 10, 11, or 12 months) and/or iv) does not receive a bronchoscopy-based procedure for biopsy of lesions to remove abnormal tissue.

[0079] Module 9 genes are provided in Table

13. At least one of the module 9 gene can be any one or more of the module 9 genes listed in Table 13. The module 9 genes are provided in Table 16. At least one module 9 gene can be any one or more of the module 9 genes listed in Table 16.

[0080] In some embodiments of any aspect, the expression level of two or more genes from module 9 is determined. In some embodiments of either aspect, the expression level of each gene from module 9 of the Table is determined. 13. In some embodiments of either aspect, the expression level of each gene in module 9 of Table 16 is determined.

[0081] In some embodiments of either aspect, at least one of the module 9 gene comprises or is EPSTI1; UBE2L6; B2M and/or TAP1. In some embodiments of either aspect, at least one of the module 9 gene comprises or is EPSTI1; UBE2L6; B2M; and TAP1. In some embodiments of either aspect, at least one of the module 9 gene comprises or is a combination of two of any of: EPSTI1 and UBE2L6 EPSTI1 and B2M EPSTI1 and TAP1 UBE2L6 and B2M UBE2L6 and TAP1 B2M and TAP1.

[0082] In some embodiments of any of the aspects, at least one of the module 9 gene comprises or is a combination of three of any of: EPSTI1; UBE2L6; and B2M EPSTI1; UBE2L6; and TAP1 EPSTI1; B2M; and TAP1 TAP1; UBE2L6; and B2M.

[0083] Module 10 genes are provided in Table

13. At least one of the module 10 gene can be any one or more of the module 10 genes listed in Table 13. In some embodiments of either aspect, the expression level of both module genes is determined.

10. In some embodiments of either aspect, at least one of the module 10 gene comprises or is CACNB3 or MAPK10. In some embodiments of either aspect, at least one of the module 10 gene comprises or is CACNB3 and MAPK10.

When an individual has a premalignant bronchial inflammatory lesion, aggressive and/or anti-inflammatory treatment may be beneficial. Accordingly, in one aspect of any of the modalities, a method of treating bronchial premalignant lesions is provided herein, the method comprising administering at least one of: i) a bronchoscopy-based procedure to examine the central airway and a chest computed tomography; ii) at least every 6 months, at least one of a bronchoscopy-based procedure to examine the central airway and a chest CT scan; and/or iii) at least one anti-inflammatory drug to a subject determined to have at least one of a) an increased expression level of at least one module 2 gene compared to a reference level; and b) a reduced expression level of at least one module 6 gene compared to a reference level. In one aspect of either embodiment, a method of treating bronchial premalignant lesions is provided herein, the method comprising determining an individual to have at least one of a) an increased expression level of at least one gene of the module 2 compared to a reference level; and b) a reduced expression level of at least one module 6 gene compared to a reference level and administering at least one of: i) a bronchoscopy-based procedure to examine the central airway and a computed tomography scan of the chest; ii) at least every 6 months, at least one of a bronchoscopy-based procedure to examine the central airway and a chest CT scan; and/or iii) at least one anti-inflammatory drug to the individual. In some modalities of either aspect, the reference level is a non-inflammatory reference level.

In some embodiments, if the individual is determined not to have at least one of a) an increased expression level of at least one module 2 gene compared to a reference level; and b) a reduced expression level of at least one module 6 gene compared to a reference level, the individual does not receive an anti-inflammatory drug and receives a bronchoscopy-based procedure to examine the central airway and/or a CT scan chest computed no more often than every 6 months (eg, no more often than every 6, 7, 8, 9, 10, 11, or 12 months).

In some embodiments, the individual is determined to lack a) an increased expression level of at least one module 2 gene compared to a reference level; and b) a reduced expression level of at least one module 6 gene compared to a reference level, the individual does not receive an anti-inflammatory drug and receives a bronchoscopy-based procedure to examine the central airway and/or a CT scan chest computed no more often than every 6 months (eg, no more often than every 6, 7, 8, 9, 10, 11, or 12 months).

[0086] The module 2 and module 6 genes are provided in Table 13. At least one module 2 and/or module 6 gene can be any one or more of the module 2 and 6 genes listed in Table 13.

[0087] In some embodiments of either aspect, the expression level of at least one gene from module 2 or at least one gene from module 6 is determined. In some embodiments of either aspect, the level of expression is determined of two or more genes from module 2 or two or more genes from module 6. In some embodiments of either aspect, the expression level of each module 2 gene or each module 6 gene of Table 13 is determined.

[0088] In some embodiments of either aspect, at least one of the module 2 gene comprises or is MSANTD2, CCNL2 or LUC7L. In some embodiments of either aspect, at least one of the module 2 gene comprises or is MSANTD2 and LUC7L. In some embodiments of either aspect, at least one of the module 2 gene comprises or is MSANTD2 and CCNL2. In some embodiments of either aspect, at least one of the module 2 gene comprises or is CCNL2 and LUC7L. In some embodiments of either aspect, at least one of the module 2 gene comprises or is MSANTD2, CCNL2 and LUC7L. In some embodiments of either aspect, at least one of the module 6 gene comprises or is NEK11 or IFT88. In some embodiments of either aspect, at least one of the module 6 gene comprises or is NEK11 and IFT88.

[0089] The inflammatory subtype is further distinguished by increased expression of module 7, 1 and/or 8 and/or decreased expression of module 4 and/or 5. Consequently, in some modalities of any of the aspects, the individual is further determined to have at least one of: i) an increased expression level of at least one module 7 gene, module 1 and/or module 8 and ii) a reduced expression level of at least one module 4 gene or module 5 compared to a reference level. In some embodiments of either aspect, the individual is further determined to have at least one of: i) an increased expression level of at least one gene from module 7, module 1 and/or module 8, and ii) a level of reduced expression of at least one module 4 or module 5 gene compared to a reference level. In some modalities of either aspect, the reference level is a non-inflammatory reference level.

[0090] Genes from modules 7, 1, 8, 4 and 5 are provided in Table 13. At least one of the gene from module 7, 1, 8, 4 and/or 5 can be any one or more of the genes from module 7 , 1, 8, 4 and/or 5 listed in Table 13. In some modalities of either aspect, the expression level of each gene from module 7, 1, 8, 4 and/or 5 of the Table is determined.

13. In some modalities of either aspect, the expression level of each gene from module 7, 1, 8, 4 and 5 of Table 13 is determined.

[0091] In some embodiments of either aspect, at least one of the module 4 gene comprises or is

COX6A1 or COX7A2. In some embodiments of either aspect, at least one of the module 4 gene comprises or is

COX6A1 and COX7A2. In some embodiments of either aspect, at least one of the module 7 gene comprises or is

RPL26 or RPL23. In some embodiments of either aspect, at least one of the module 7 gene comprises or is

RPL26 and RPL23. In some embodiments of either aspect, at least one of the module 5 gene comprises or is

RACGAP1 or TPX2. In some embodiments of either aspect, at least one of the module 5 gene comprises or is

RACGAP1 and TPX2. In some embodiments of either aspect, at least one of the module 1 gene comprises or is

KIRREL; PHLDB1; or MARVELD1. In some embodiments of either aspect, at least one of the module 1 gene comprises or is PHLDB1 and MARVELD1. In some embodiments of either aspect, at least one of the module 1 gene comprises or is KIRREL and PHLDB1. In some embodiments of either aspect, at least one of the module 1 gene comprises or is KIRREL and MARVELD1. In some embodiments of either aspect, at least one of the module 1 gene comprises or is KIRREL; PHLDB1; and MARVELD1. In some embodiments of either aspect, at least one of the module 8 gene comprises or is DCO2; CD53; or LAPTM.

In some embodiments of either aspect, at least one of the module 8 gene comprises or is CD53 and LAPTM. In some embodiments of either aspect, at least one of the module 8 gene comprises or is DCO2 and CD53. In some embodiments of either aspect, at least one of the module 8 gene comprises or is DCO2 and LAPTM. In some embodiments of either aspect, at least one of the module 8 gene comprises or is DCO2; CD53; and LAPTM.

[0092] In some modalities of any of the aspects, the expression level of each of the genes in Table 15 is determined. In some modalities of any of the aspects, the expression level of each of the genes in Table 15 is determined. in a bronchial smear sample.

[0093] In some modalities of any of the aspects, the expression level of each of the genes in Table 14 is determined. In some modalities of any of the aspects, the expression level of each of the genes in Table 14 is determined. in a bronchial smear sample.

[0094] In some embodiments of any of the aspects, the methods described in this document may further comprise determining the expression level of any of the following genes: SOX2, NFE2L2, PIK3CA (which are squamous cancer marker genes), KRT5 , MUC5AC, TUB1A1, SCGB1A1 and FOXK1 (which are epithelial marker genes).

[0095] As described in this document, gene expression levels can be modulated (eg, increased or decreased) in individuals with pre-malignant lesions of different subtypes.

In some embodiments of either aspect, the method comprises administering a treatment described herein to an individual previously determined to have an expression level as described herein. In some embodiments of either aspect, a method of treating bronchial premalignant lesions in an individual in need thereof is described herein, the method comprising: a) first determining the expression level of at least one gene in a sample obtained from an individual; and b) then administering a treatment as described herein to the subject if the level of expression is modulated relative to a reference in the manner described herein. In one aspect of any of the modalities, a method of treating bronchial premalignant lesions in an individual in need thereof is described herein, the method comprising: a) determining whether the individual has a modulation of an expression level as described herein and b) instructing or directing the individual to receive the appropriate treatment described herein for the particular modulation of expression that has been determined.

[0097] In some modalities of any of the aspects, the step of determining whether the individual has modulation of an expression level may comprise i) obtaining or having obtained a sample from the individual and ii) performing or having performed an assay on the obtained sample of the individual to determine/measure the level of expression in the individual. In some embodiments of either aspect, the step of determining whether the subject has a modulation of an expression level may comprise performing or having performed an assay on a sample obtained from the subject to determine/measure the expression level in the subject. In some embodiments of either aspect, the step of determining whether the subject has a modulation of an expression level may comprise ordering or ordering an assay on a sample obtained from the subject to determine/measure the expression level in the subject. In some embodiments of either aspect, the step of determining whether the subject has a modulation of an expression level may comprise receiving the results of an assay on a sample obtained from the subject to determine/measure the expression level in the subject. In some embodiments of either aspect, the step of determining whether the individual has a one-level modulation of expression may comprise receiving a report, results, or other means of identifying the individual as an individual with a one-level modulation.

[0098] In some modalities of any of the aspects, the step of instructing or guiding the individual to receive a specific treatment may comprise providing a report of the results of the trial. In some embodiments of either aspect, the step of instructing or directing the individual to receive a specific treatment may comprise providing a report of the trial results and/or treatment recommendations in view of the trial results.

[0099] In some embodiments of any of the aspects, measuring the level of a target and/or detecting the level or presence of a target, for example, an expression product (nucleic acid or polypeptide from one of the genes described in the document) or a mutation may comprise a transformation. As used herein, the term "transform" or "transformation" refers to changing an object or substance, eg, biological sample, nucleic acid or protein, into another substance. The transformation can be physical, biological or chemical. The exemplary physical transformation includes,

but without limitations, pre-treatment of a biological sample, eg whole blood to blood serum by differential centrifugation. A biological/chemical transformation may involve the action of at least one enzyme and/or chemical reagent in a reaction. For example, a DNA sample can be digested into fragments by one or more restriction enzymes, or an exogenous molecule can be ligated to a fragmented DNA sample with a ligase.

In some modalities of either aspect, a DNA sample can undergo enzymatic replication, for example, through polymerase chain reaction (PCR).

[0100] Transformation, measurement and/or detection of a target molecule, for example, an mRNA or polypeptide, may comprise contacting a sample obtained from an individual with a reagent (for example, a detection reagent) that is specific for the target , for example, a target-specific reagent. In some embodiments of either aspect, the target-specific reagent is detectably labeled. In some embodiments of either aspect, the target-specific reagent is capable of generating a detectable signal. In some embodiments of either aspect, the target-specific reagent generates a detectable signal when the target molecule is present.

[0101] Methods for measuring gene expression products are known to those skilled in the art. Such methods for measuring gene expression products, eg protein level, include ELISA (enzyme-linked immunosorbent assay), Western blot, immunoprecipitation and immunofluorescence using detection reagents such as an antibody or protein-binding agents.

Alternatively, a peptide can be detected in an individual by introducing a labeled anti-peptide antibody and other types of detection agent. For example, the antibody can be labeled with a detectable marker whose presence and location in the individual is detected by standard imaging techniques.

[0102] For example, antibodies to the various targets described herein are commercially available and can be used for purposes of the invention to measure protein expression levels. Alternatively, since the amino acid sequences for the targets described herein are known and publicly available on the NCBI website, those skilled in the art can raise their own antibodies against these polypeptides of interest for purposes of the methods described herein.

[0103] The amino acid sequences of the polypeptides described in this document have been assigned the accession numbers NCBI and ENSBL for different species, such as humans, mice and rats. Sequences for any of the genes described herein can be easily retrieved from any database by those skilled in the art. In some embodiments of either aspect, the sequence of a gene, transcript or polypeptide described herein is the sequence available in the NCBI or ENSMBL database as of the filing date of this application.

[0104] In some embodiments of either aspect, immunohistochemistry ("IHC") and immunocytochemistry ("ICC") techniques may be used. IHC is the application of immunochemistry to tissue sections, while ICC is the application of immunochemistry to cells or tissue prints after they have been subjected to specific cytological preparations such as, for example, liquid-based preparations. Immunochemistry is a family of techniques based on the use of an antibody, in which antibodies are used to specifically target molecules in or on the surface of cells. The antibody typically contains a marker that will undergo a biochemical reaction and thus experience a color change upon encountering the target molecules. In some cases, signal amplification can be integrated into the particular protocol, where a secondary antibody, which includes the spot or marker signal, follows application of a specific primary antibody.

[0105] In some embodiments of either aspect, the assay may be a Western blot analysis.

Alternatively, proteins can be separated by two-dimensional gel electrophoresis systems. Two-dimensional gel electrophoresis is well known in the art and typically involves isoelectric focusing along a first dimension followed by SDS-PAGE electrophoresis along a second dimension. These methods also require a considerable amount of cellular material. Analysis of 2D SDS-PAGE gels can be performed by determining the intensity of protein spots on the gel or can be performed using immune detection. In other modalities, protein samples are analyzed using mass spectroscopy.

[0106] Immune tests can be used with the methods and assays described herein and include, for example, competitive and non-competitive assay systems using techniques such as Western blots, radioimmunoassay (RIA), ELISA (enzyme immunoassay), immunoassays in "sandwich", immunoprecipitation assays, immunodiffusion assays, agglutination assays, for example, latex agglutination, complement fixation assays, immunoradiometric assays, fluorescent immunoassays, for example, FIA (fluorescence-linked immunoassay), chemiluminescence immunoassays ( CLIA), electrochemiluminescence immunoassay (ECLIA), counting immunoassay (CIA), lateral flow immunoassays (LFIA), magnetic immunoassay (MIA), and protein A immunoassays.

Methods for performing such assays are known in the art, provided an appropriate antibody reagent is available. In some embodiments of either aspect, the immunoassay can be a quantitative or semiquantitative immunoassay.

[0107] An immunoassay is a biochemical test that measures the concentration of a substance in a biological sample, typically a fluid sample such as blood or serum, using the interaction of an antibody or antibodies by its antigen. The assay takes advantage of the highly specific binding of an antibody to its antigen. For the methods and assays described herein, specific binding of target polypeptides to respective proteins or protein fragments, or an isolated peptide, or a fusion protein described herein, occurs in the immunoassay to form a protein/peptide complex target. The complex is then detected by a variety of methods known in the art. An immunoassay also often involves the use of a detection antibody.

[0108] The enzyme-linked immunosorbent assay, also called ELISA, enzyme immunoassay, or EIA, is a biochemical technique used primarily in immunology to detect the presence of an antibody or antigen in a sample. ELISA has been used as a diagnostic tool in medicine and phytopathology, as well as quality control verification in several industries.

[0109] In one embodiment, an ELISA involving at least one antibody with specificity for the particular desired antigen (eg, any of the targets as described herein) can also be performed.

A known amount of sample and/or antigen is immobilized on a solid support (usually a polystyrene microtiter plate). Immobilization can be non-specific (eg, through surface adsorption) or specific (eg, where another antibody immobilized on the surface is used to capture the antigen or a primary antibody). After immobilization of the antigen, the detection antibody is added, forming a complex with the antigen. The detecting antibody can be covalently linked to an enzyme or it can be detected itself by a secondary antibody that is linked to an enzyme through bioconjugation. Between each step, the plate is typically washed with a neutral detergent solution to remove any proteins or antibodies that are not specifically bound. After the final washing step, the plate is developed with the addition of an enzyme substrate to produce a visible signal, which indicates the amount of antigen in the sample. Older ELISAs use chromogenic substrates, although newer assays use fluorogenic substrates with much greater sensitivity.

[0110] In another modality, a competitive ELISA is used. Purified antibodies that are directed against a target polypeptide or fragment thereof are coated onto the solid phase of the multi-well plate, i.e., conjugated to a solid surface. A second batch of purified antibodies that are not conjugated to any solid support is also required. These unconjugated purified antibodies are labeled for detection purposes, for example, labeled with horseradish peroxidase to produce a detectable signal. A sample (eg, a blood sample) from an individual is mixed with a known amount of the desired antigen (eg, a known volume or concentration of a sample that comprises a target polypeptide) along with the horseradish peroxidase labeled antibodies. and the mixture is then added to the coated wells to form a competitive blend. After incubation, if the level of polypeptide is high in the sample, a labeled antibody-reagent-antigen complex will form. This complex is free in solution and washable. Washing the cavities will remove the complex. The wells are then incubated with TMB color development substrate (3,3',5,5'-tetramethylbenzidene) for localization of horseradish peroxidase conjugated antibodies in the wells. There will be little or no color change if the target polypeptide level is high in the sample. If there is little or no target polypeptide present in the sample, a different complex is formed, the solid support complex bound to antibody-target polypeptide reagents. This complex is immobilized on the plate and is not washed in the washing step.

Subsequent incubation with TMB will produce a significant color change. This competitive ELISA assay is specific, sensitive, reproducible and easy to operate.

[0111] There are other different forms of ELISA that are well known to those skilled in the art. Standard methods known in the art for ELISA are described in "Methods in Immunodiagnosis", 2nd edition, Rose and Bigazzi, eds. John Wiley & Sons, 1980; and Oellerich, M. 1984, J. Clin.

Chem. Clin. Biochem. 22: 895-904. These references are incorporated herein by reference in their entirety.

[0112] In one embodiment, levels of a polypeptide in a sample can be detected using a lateral flow immunoassay (LFIA) test, also known as an immunochromatographic assay or strip test. LFIAs are simple devices designed to detect the presence (or absence) of antigen, eg, a polypeptide, in a fluid sample. Currently, there are many LFIA tests used for medical diagnosis, whether for home testing, point-of-care testing, or laboratory use.

LFIA tests are a form of immunoassay in which the test sample flows along a solid substrate through capillary action. After the sample is applied to the test strip, it finds a colored reagent (usually comprising antibody specific for the test target antigen) bound to microparticles that mixes with the sample and travels through the substrate finding lines or zones that have been pretreated with another antibody or antigen. Depending on the level of target polypeptides present in the sample, the colored reagent can be captured and connected to the test line or zone. LFIAs are essentially immunoassays adapted to operate along a single axis to fit the shape of the test strip or rod. Strip tests are extremely versatile and can be easily modified by those skilled in the art to detect a wide variety of antigens from fluid samples such as urine, blood, water and/or homogenized tissue samples etc. Strip tests are also known as dipstick tests, the name derived from the literal action of "dipping" the test strip into a sample of fluid to be tested. LFIA strip tests are easy to use, require minimal training, and can be easily included as diagnostic point-of-care (POCT) testing components to be used onsite in the field. LFIA tests can be operated as competitive or sandwich tests. Sandwich LFIAs are similar to the sandwich ELISA. First, the sample finds colored particles that are tagged with antibodies raised to the target antigen. The test line will also contain antibodies to the same target, although it may bind to a different epitope on the antigen. The test line will be displayed as a colored band on positive samples.

In some embodiments of either aspect, the lateral flow immunoassay can be a dual antibody sandwich assay, a competitive assay, a quantitative assay, or variations thereof. Competitive LFIAs are similar to the competitive ELISA. First, the sample finds colored particles that are tagged with the target antigen or an analogue. The test line contains antibodies to the target/analog thereof. Unlabeled antigen in the sample will block binding sites on the antibodies, preventing absorption of the colored particles. The test line will be displayed as a colored band on negative samples. There are several variations in lateral flow technology. It is also possible to apply multiple capture zones to create a multiplex test.

[0113] The use of "dip sticks" or LFIA test strips and other solid supports have been described in the art in the context of an immunoassay for a number of antigen biomarkers. U.S. Patent Nos. 4,943,522; 6,485,982; 6,187,598; 5,770,460; 5,622,871; 6,565,808, U.S. Patent Application No. 10/278,676; U.S. Patent No. 09/579,673 and U.S. Patent No. 10/717,082, which are incorporated herein by reference in their entirety, are non-limiting examples of such lateral flow test devices.

Examples of patents describing the use of "dip stick" technology to detect soluble antigens through immunochemical assays include, but are not limited to, U.S. Patent Nos. 4,444,880; 4,305,924; and 4,135,884; which are incorporated by reference into this document in its entirety. The devices and methods of these three patents broadly describe a first component affixed to a solid surface on a "dip stick", which is exposed to a solution containing a soluble antigen that binds to the component affixed to the "dip stick", prior to detection of the component-antigen complex on the rod. It is within the skill of those skilled in the art to modify the teachings of this "dip stick" technology for the detection of polypeptides using antibody reagents as described herein.

[0114] Other techniques can be used to detect the level of a polypeptide in a sample. One such technique is dot blot, an adaptation of the Western blot (Towbin et al., Proc. Nat. Acad. Sci. 76: 4350 (1979)). In a Western blot, the polypeptide or fragment thereof can be dissociated with detergents and heat and separated on an SDS-PAGE gel before being transferred to a solid support such as a nitrocellulose or PVDF membrane. The membrane is incubated with an antibody reagent specific for the target polypeptide or a fragment thereof. The membrane is then washed to remove unbound proteins and non-specifically bound proteins. Detectably labeled secondary detection or enzyme-linked antibodies can then be used to detect and assess the amount of polypeptide in the test sample. A dot blot immobilizes a protein sample on a defined region of a support which is then hybridized with antibody and labeled secondary antibody as in the Western blot. The signal intensity of the detectable marker in any format corresponds to the amount of enzyme present and, therefore, to the amount of polypeptide. Levels can be quantified, for example, using densitometry.

[0115] In some embodiments of either aspect, the level of a target can be measured, by way of non-limiting example, by means of Western blot; immunoprecipitation; enzyme-linked immunosorbent assay (ELISA); radioimmunoassay (RIA); sandwich essay; Fluorescent in situ hybridization (FISH); immunohistological staining; radioimmunometric assay; immunofluorescence assay; mass spectroscopy and/or immunoelectrophoresis assay.

[0116] In certain embodiments, gene expression products as described herein may be determined, instead, by determining the level of messenger RNA (mRNA) expression of the genes described herein. These molecules can be isolated, derived or amplified from a biological sample,

such as a blood sample. Techniques for detecting mRNA expression are known to those of skill in the art and may include, but are not limited to, PCR procedures, RT-PCR, Northern blot analysis, quantitative RT-PCR, differential gene expression, RNAse protection assay , microarray-based analysis, state-of-the-art sequencing; hybridization methods, etc.

[0117] In general, the PCR procedure describes a method of gene amplification that comprises (i) sequence-specific hybridization of primers to specific genes or sequences within a nucleic acid sample or library, (ii) subsequent amplification involving multiple cycles of annealing, elongation and denaturation using a thermostable DNA polymerase and (iii) screening the PCR products for a band of the correct size. The primers used are oligonucleotides of sufficient length and appropriate sequence to allow the initiation of polymerization, that is, each primer is specifically designed to be complementary to a stretch of the genomic locus to be amplified. In an alternative embodiment, the mRNA level of the gene expression products described herein can be determined using reverse transcription PCR (RT) and quantitative RT-PCR (QRT-PCR) or real-time PCR methods. RT-PCR and QRT-PCR methods are well known in the art.

[0118] In some embodiments of either aspect, the level of an mRNA can be measured using a quantitative sequencing technology, for example, a state-of-the-art quantitative sequencing technology.

Methods of sequencing a nucleic acid sequence are well known in the art. Briefly, a sample obtained from an individual can be contacted with one or more primers that specifically hybridize to a single-stranded nucleic acid sequence that flanks the target gene sequence and a complementary strand is synthesized. In some second generation technologies, an adapter (single or double stranded) is attached to nucleic acid molecules in the sample and synthesis proceeds from the adapter or primers compatible with the adapter. In some third-generation technologies, the sequence can be determined, for example, by determining the location and pattern of probe hybridization or measuring one or more characteristics of a single molecule as it passes through a sensor (eg, the modulation of an electric field when a nucleic acid molecule passes through a nanopore).

Exemplary sequencing methods include, but are not limited to, Sanger sequencing, dideoxy chain termination, high-throughput sequencing, next-generation sequencing, 454 sequencing, SOLiD sequencing, Polony sequencing, Illumina sequencing, Ion Torrent sequencing, hybridization sequencing, sequencing Nanopore, Helioscope sequencing, real-time single-molecule sequencing, RNAP sequencing, and so on. Methods and protocols for performing these sequencing methods are known in the art; see, for example, "Next Generation Genome Sequencing", Ed. Michal Janitz, Wiley-VCH; Eds. "High-Throughput Next Generation Sequencing", Eds. Kwon and Ricke, Humanna Press, 2011; and Sambrook et al., Molecular Cloning: A Laboratory Manual (4th ed.), Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y., USA (2012); which are incorporated by reference into this document in its entirety.

[0119] Nucleic acid sequences of the genes described in this document have been assigned the NCBI and ENSBL accession numbers for different species, such as human, mouse and rat. Sequences for any of the genes described herein can be easily retrieved from any database by those skilled in the art. In some embodiments of either aspect, the sequence of a gene, transcript or polypeptide described herein is the sequence available in the NCBI or ENSMBL database as of the filing date of this application. Consequently, those skilled in the art can design an appropriate primer based on the known sequence to determine the mRNA level of the respective gene.

[0120] Nucleic acid and ribonucleic acid (RNA) molecules can be isolated from a particular biological sample using any of a number of procedures, which are well known in the art, the isolation procedure chosen in particular being appropriate for the sample biological in particular. For example, freeze-thaw and alkaline lysis procedures can be useful for obtaining nucleic acid molecules from solid materials; alkaline and thermal lysis procedures can be useful for obtaining nucleic acid molecules from urine; and proteinase K extraction can be used to obtain nucleic acid from blood (Roiff, A. et al.

PCR: Clinical Diagnostics and Research, Springer (1994)).

[0121] In some embodiments of any of the aspects, one or more of the reagents (e.g., an antibody reagent and/or nucleic acid probe) described herein may comprise a detectable marker and/or comprise the ability to generate a detectable signal (eg, by catalyzing the reaction of converting a compound to a detectable product). Detectable labels can comprise, for example, a light-absorbing dye, a fluorescent dye or a radioactive label. Detectable markers, methods for detecting them, and methods for incorporating them into reagents (for example, antibodies and nucleic acid probes) are well known in the art.

[0122] In some embodiments of either aspect, detectable markers may include markers that can be detected by spectroscopic, photochemical, biochemical, immunochemical, electromagnetic, radiochemical or chemical means, such as fluorescence, chemofluorescence or chemiluminescence or any other appropriate means . The detectable labels used in the methods described herein can be primary labels (where the label comprises a moiety that is directly detectable or that produces a directly detectable moiety) or secondary labels (where the detectable label binds to another moiety to produce a signal detectable, for example, as is common in immunolabeling using secondary and tertiary antibodies). The detectable label can be attached to the reagent through covalent or non-covalent means. Alternatively, a detectable label can be attached, for example, by directly labeling a molecule that achieves binding to the reagent via a binding ligand-receptor binding pair configuration or other specific recognition molecules.

Detectable markers can include, but are not limited to, radioisotopes, bioluminescent compounds, chromophores, antibodies, chemiluminescent compounds, fluorescent compounds, metal chelates and enzymes.

[0123] In other embodiments, the detection reagent is labeled with a fluorescent compound. When the fluorescently labeled reagent is exposed to light of the proper wavelength, its presence can then be detected by virtue of the fluorescence. In some embodiments of either aspect, a detectable marker can be a fluorescent dye molecule or fluorophore including, but not limited to, fluorescein, phycoerythrin, phycocyanin, ophthaldehyde, fluorescamine, Cy3TM, Cy5TM, allophycocyanin, Texas Red, chlorophyll peridenine, cyanine, tandem conjugates such as phycoerythrin-Cy5TM, green fluorescent protein, rhodamine, fluorescein isothiocyanate (FITC) and Oregon GreenTM, rhodamine and derivatives (e.g. Texas Red and tetrarodymine isothiocyanate (TRITC)), biotin, phycoerythrin, AMCA, CyDyesTM, 6-carboxyfluorescein

(commonly known by the abbreviations FAM and F), 6-carboxy-

2',4',7',4,7-hexachlorofluorescein (HEX), 6-carboxy-4',5'-

dichloro-2',7'-dimethoxyfluorescein (JOE or J), N,N,N',N'-

tetramethyl-6carboxyrhodamine (TAMRA or T), 6-carboxy-X-

rhodamine (ROX or R), 5-carboxyrhodamine-6G (R6G5 or G5), 6-

carboxyrhodamine-6G (R6G6 or G6) and rhodamine 110; cyanine dyes, for example Cy3, Cy5 and Cy7 dyes; coumarins,

for example, umbelliferone; benzmide dyes, for example, Hoechst 33258; phenanthridine dyes, for example Texas Red; ethidium dyes; acridine dyes;

carbazole dyes; fenoxazine dyes; porphyrin dyes; polymethine inks, for example cyanine dyes such as Cy3, Cy5, etc.; BODIPY dyes and quinoline dyes.

In some embodiments of either aspect, a detectable marker may be a radioactive marker including, but not limited to,

3H, 125I, 35S, 14C, 32P and 33P.

In some embodiments of either aspect, a detectable marker can be an enzyme including, but not limited to, horseradish peroxidase and alkaline phosphatase.

An enzyme label can produce, for example, a chemiluminescent signal, a color signal or a fluorescent signal.

Enzymes considered for use to detectably label an antibody reagent include, but are not limited to, malate dehydrogenase, staphylococcal nuclease, delta-V-steroid isomerase, yeast alcohol dehydrogenase, alpha-glycerophosphate dehydrogenase, triose phosphate isomerase, horseradish peroxidase , alkaline phosphatase, asparaginase, glucose oxidase, beta-galactosidase, ribonuclease, urease, catalase, glucose VI-phosphate dehydrogenase, glucoamylase and acetylcholinesterase. In some embodiments of either aspect, a detectable marker is a chemiluminescent marker including, but not limited to, lucigenin, luminol, luciferin, isoluminol, theromatic acridinium ester, imidazole, acridinium salt, and oxalate ester. In some embodiments of either aspect, a detectable marker may be a spectral colorimetric marker including, but not limited to, colloidal gold spheres or colored glass or plastic (eg, polystyrene, polypropylene, and latex).

[0124] In some embodiments of either aspect, detection reagents may also be labeled with a detectable label, such as c-Myc, HA, VSV-G, HSV, FLAG, V5, HIS, or biotin. Other detection systems can also be used, for example a biotin-streptavidin system. In this system, antibodies immunoreactive (i.e., specific for) with the biomarker of interest are biotinylated. The amount of biotinylated antibody bound to the biomarker is determined using a streptavidin-peroxidase conjugate and a chromogenic substrate. These streptavidin peroxidase detection kits are commercially available, for example, from DAKO; Carpentry, CA. A reagent can also be detectably labeled using metals that emit fluorescence, such as 152 Eu, or others of the lanthanide series. These metals can be bonded to the reagent using metal chelating groups such as diethylenetriamine pentaacetic acid (DTPA) or ethylenediaminetetraacetic acid (EDTA).

[0125] In some embodiments of either aspect, the expression level is the level in a sample obtained from an individual. The term "sample" or "test sample" as used herein denotes a sample taken or isolated from a biological organism, for example, a sample of blood or tissue from an individual. In some embodiments of either aspect, the present invention encompasses various examples of a biological sample. In some embodiments of either aspect, the biological sample is cells, or tissue, or peripheral blood, or bodily fluid. Exemplary biological samples include, but are not limited to, a biopsy, a tumor sample, a biological fluid sample; blood; serum; plasma; urine; sperm; mucus; tissue biopsy; organ biopsy; synovial fluid; biliary fluid; cerebrospinal fluid; mucosal secretion; effusion; sweat; Spittle; and/or tissue sample, etc. The term also includes a mixture of the aforementioned samples. The term "test sample" also includes untreated or pretreated (or preprocessed) biological samples. In some embodiments of either aspect, a test sample may comprise cells from an individual. In some embodiments of either aspect, the sample obtained from an individual may be a biopsy sample. In some embodiments of either aspect, the sample obtained from an individual may be a blood or serum sample.

[0126] In some modalities of either aspect, the sample is an endobronchial biopsy, bronchial smear sample, bronchial biopsy, endobronchial smear sample, upper airway biopsy, upper airway smear sample, nasal epithelial cells, sputum and/or blood obtained from the individual. In some modalities of either aspect, the sample is a bronchial smear taken from the right or left main bronchus. The test sample can be obtained by removing a sample from an individual, but it can also be performed using a previously isolated sample.

(eg isolated at a previous point in time and isolated by the same person or another person).

[0127] In some embodiments of either aspect, the test sample may be an untreated test sample. As used herein, the phrase "untreated test sample" refers to a test sample that has not had any pretreatment of the sample except for dilution and/or suspension in a solution.

Exemplary methods for treating a test sample include, but are not limited to, centrifugation, filtration, sonication, homogenization, heating, freezing and thawing, and combinations thereof. In some embodiments of either aspect, the test sample may be a frozen test sample, for example, a frozen tissue. The frozen sample can be thawed prior to employing the methods, assays, and systems described in this document. After thawing, a frozen sample can be centrifuged before being subjected to the methods, assays and systems described in this document. In some embodiments of either aspect, the test sample is a clarified test sample, for example, by means of centrifugation and collection of a supernatant comprising the clarified test sample. In some embodiments of either aspect, a test sample may be a pre-processed test sample, for example, supernatant or filtrate resulting from a treatment selected from the group consisting of centrifugation, filtration, thawing, purification, and any combinations thereof. In some embodiments of either aspect, the test sample may be treated with a chemical and/or biological reagent.

Chemical and/or biological reagents can be employed to protect and/or maintain the stability of the sample, including biomolecules (eg, nucleic acids and protein) in it, during processing. An exemplary reagent is a protease inhibitor, which is generally used to protect or maintain protein stability during processing. Those of skill in the art are well aware of the appropriate methods and procedures for pre-processing biological samples necessary for determining the level of an expression product, as described herein.

[0128] In some modalities of any of the aspects, the methods, tests and systems described in this document may further comprise a step of obtaining a test sample from an individual. In some modalities of either aspect, the individual can be a human being. In some embodiments of either aspect, the individual may be an individual in need of treatment for (for example, who has or has been diagnosed as having) pre-malignant lesions or an individual at risk or at increased risk of developing pre-malignant lesions bronchial disorders, as described elsewhere in this document.

[0129] In some embodiments of either aspect, the biopsy sample or smear comprises morphologically normal tissues or cells, for example, the tissues or cells are not from a lesion and have normal morphology as to their location in vivo. In some embodiments of either aspect, the biopsy or smear sample consists essentially of morphologically normal tissue or cells. In some modalities of either aspect, the biopsy or smear sample consists of morphologically normal tissue or cells.

[0130] In some embodiments of either aspect, the biopsy or smear sample comprises visually normal tissues or cells, for example, the tissues or cells are not from a lesion and appear normal to the naked eye. localization. In some modalities of either aspect, the biopsy sample or smear consists essentially of visually normal tissue or cells. In some modalities of either aspect, the biopsy specimen or smear consists of visually normal tissue or cells.

[0131] In some modalities of either aspect, the biopsy or smear sample comprises premalignant bronchial lesion cells. In some modalities of either aspect, the biopsy specimen or smear consists essentially of premalignant bronchial lesion cells. In some modalities of either aspect, the biopsy specimen or smear consists of cells from a premalignant bronchial lesion.

[0132] A level that is lower than a reference level can be a level that is lower by at least about 10%, at least about 20%, at least about 50%, at least about 60%, at least about 80%, at least about 90% or less of the reference level. In some modalities of either aspect, a level that is less than a reference level may be a level that is statistically significantly less than the reference level.

[0133] A level that is greater than a reference level may be a level that is greater by at least about 10%, at least about 20%, at least about 50%, at least about 60%, at least about 80%, at least about 90%, at least about 100%, at least about 200%, at least about 300%, at least about 500% or more relative to the reference level. In some modalities of either aspect, a level that is higher than a reference level may be a level that is statistically significantly higher than the reference level.

[0134] In some embodiments of either aspect, the reference may be a target molecule level in a population of individuals who do not or have not been diagnosed as having and/or do not exhibit signs or symptoms of premalignant bronchial lesions. In some embodiments of either aspect, the reference may also be an expression level of the target molecule in a control sample, a pooled sample of control individuals, or a numerical value or range of values based on it. In some embodiments of either aspect, the reference may be the level of a target molecule in a sample obtained from the same individual at an earlier point in time, for example, the methods described herein may be used to determine whether sensitivity or an individual's response to a particular therapy changes over time or the subtype of their lesions is changing.

[0135] In some embodiments of either aspect, the level of expression products of no more than 200 other genes is determined. In some embodiments of either aspect, the level of expression products of no more than 100 other genes is determined. In some embodiments of either aspect, the level of expression products of no more than 20 other genes is determined. In some embodiments of either aspect, the level of expression products of no more than 10 other genes is determined.

[0136] In some embodiments of the foregoing aspects, the expression level of a particular gene may be normalized relative to the expression level of one or more reference genes or proteins.

[0137] In some embodiments, the reference level may be the level in a sample of a similar cell type, sample type, sample processing and/or obtained from an individual of age, sex, and other demographic parameters similar to those of the sample/individual for which the expression level is to be determined. In some embodiments, the test sample and the reference control sample are of the same type, that is, obtained from the same biological source and comprising the same composition, for example, the same number and type of cells.

[0138] In some embodiments of either aspect, the reference level can be a non-proliferative reference level, for example, the level in a tissue or cell that does not comprise a proliferative lesion or of an individual that does not have a lesion. proliferative. For example, the level can be the level of inflammatory, secretory, or normal lesion subtypes or an average or grouping thereof.

[0139] In some embodiments, the methods described herein refer to the treatment of an individual who has or has been diagnosed as having premalignant bronchial lesions. Individuals who have premalignant bronchial lesions can be identified by a physician using current methods of diagnosing premalignant bronchial lesions. Tests that can aid in the diagnosis of, for example, premalignant bronchial lesions include, but are not limited to, bronchoscopy, autofluorescent bronchoscopy, etc. A family history of premalignant bronchial lesions or exposure to risk factors for premalignant bronchial lesions (eg, cigarette smoke) can also help determine whether an individual is likely to have premalignant bronchial lesions or make a diagnosis of bronchial premalignant lesions.

The compositions and methods described herein can be administered to a subject who has or has been diagnosed as having pre-malignant bronchial lesions.

In some embodiments, the methods described herein comprise administering an effective amount of the compositions described herein to a subject to alleviate a symptom of the premalignant bronchial lesions. As used herein, "alleviating a symptom of premalignant bronchial lesions" is ameliorating any condition or symptom associated with premalignant bronchial lesions.

Compared to an equivalent untreated control, this reduction is at least 5%, 10%, 20%, 40%, 50%, 60%, 80%, 90%, 95%, 99% or more as measured by means of any standard technique. A variety of means for administering the compositions described herein to individuals are known to those skilled in the art.

Such methods may include, but are not limited to, oral, parenteral, intravenous, intramuscular, subcutaneous, transdermal, airway (aerosol), pulmonary, cutaneous, topical, injection, or intratumoral administration. Administration can be local or systemic.

[0141] The methods described herein can prevent, delay or slow the development of lung cancer, eg, squamous cell carcinoma of the lung. In some embodiments of either aspect, the individual treated in accordance with the present methods is not a lung cancer individual. In some embodiments of either aspect, the individual treated in accordance with the present methods is an individual who does not have lung cancer. In some embodiments of either aspect, the individual treated in accordance with the present methods is an individual who does not have and has not had lung cancer. In some embodiments of either aspect, the individual treated in accordance with the present methods is at risk for lung cancer. In some modalities of either aspect, the individual is an individual who has a premalignant bronchial lesion.

[0142] In some modalities of either aspect, the individual is a smoker. In some forms of either aspect, the individual is an ex-smoker. In some modalities of either aspect, the individual is a non-smoker.

[0143] The treatments described herein, for example an anti-proliferative drug, anti-inflammatory drug or immunostimulating drug can be administered systemically, via inhalation and/or topically to any part of an individual's airways (including the nose and the mouth). In some embodiments of either aspect, a treatment described herein, for example, an anti-proliferative, anti-inflammatory or immunostimulant drug may be administered i) systemically and ii) via inhalation or topically to any part of the airway of a subject (including the nose and mouth) during a bronchoscopy or smear

[0144] An antiproliferative drug is a drug that inhibits cell growth and/or division, for example, cytostatic agents, where this is the primary activity of the compound in the relevant context. Non-limiting examples of anti-proliferative drugs may include CDK inhibitors (for example, purvalanol-a, palbociclib, ribociclib, abemaciclib and olomoucin II); HDAC inhibitors (for example, THM-I-94, vorinostat, givinostat); PARP inhibitors (for example AG-14361, olaparib, rucaparib, niraparib, talazoparib, veliparib, pamiparib, CEP 9722, E7016, iniparib, 3-aminobenazmide); JAK inhibitors (e.g., JAK3-VI inhibitor, ruxolitinib, tofacitinib, oclacitinib, baricitinib, peficitinib, filgotinib, cerdulatinib, gandotinib, lestaurtinib,elotinib, momritinib, PF-04965842, cucitinib, upurbatinib); JNK inhibitors (for example ZG-10, AS-601245, AM-111); MTOR inhibitors (eg AZD-8055, PI-103,

rapamycin, tensirolimus, everolimus, ridaforolimus,

rapálogues, sirolimus); FLT3 inhibitors (eg,

lestaurtinib, TG-101348, gilteritinib, quizartinib,

midostaurin, sorafenib, sunitinib); PI3K Inhibitors

(eg, GDC-0941, PI-828, wortmannin, LY294002,

hibiscon C, idelalisibe, copanlisibe, duvelisibe,

alpelisibe, taselisibe, perifosine, buparlisibe,

umbralisibe, PX-866, dactolisibe, CUDC-907, voxtalisibe;,

IPI-549, SF1126, PR6530, INK1117, pictilisibe, XL147,

palmoid 529, GSK1059615, ZSTK474, PWT33597, IC87114, TG100-

115, CAL263, RP6503, PI-103, GNE-477, AEZS-136); AKT inhibitors (eg A-443644, pyrvinium pamoate, VQD-002,

perifosine, miltefosine, MK-2206, AZD5363, ipataseritibe);

Tyrosine kinase inhibitors (eg,

aminopurvalanol-a, SU-11652, imatinib, gefitinib,

erlotinib, sunitinib, adavosertib, lapatinib);

Protein kinase inhibitors (eg HG-5-113-01,

adavosertib, afatinib, axitinib, bosuntinib, cetuximab,

conbimetinib, crizotinib, cabozantinib, dasatinib,

entrectinib, erdafitinib, erlotinib, fostamatinib,

iibrutinib, laputinib, laputinib, nilotinib, pazopanib,

pegaptanib, ruxolitinib, sorafenib, sunitinib, SU6656,

vandetanib, vemurafenib); RNA polymerase inhibitors

(for example, dactinomycin, triptolide); Topoisomerase inhibitors (eg, pidorubicin, doxorubicin,

campothecins, indenosioquinolines, indotecan,

imdimitecan, ansacrine, etoposide, teniposide, ICRF-193,

genistein); HSP inhibitors (eg inhibitor of

HSP90, 17-N-Allylamino-17-desmethoxygeldanamycin (17AAG),

gamitrinib); DNA protein kinase inhibitors (for example, PIK-75); Focal adhesion kinase inhibitors (eg PF-562271, PF573.228, PF-271, NVP-226, Y15, PND-

1186, GSK2256098, VS-6062, VS-6063, VS-4718); RNA synthesis inhibitor (daunorubicin); Inhibitor of mediator release (eg, ER-27319); and EZH2 Inhibitors

(DZNep, EPZ005687, EI1, GSK126, UNC1999, EPZ-6438,

tazemethostat). Other non-limiting examples of antiproliferative drugs include acetylcholine receptor antagonists (eg clozapine, quetiapine, atropine,

benztropine, biperiden, chlorpheniramine, citalopram,

diclomine, dimenthydrinate, diphenhydramine, doxepin,

doxylamine, glycopyrrolamine, glycopyrrone, glycopyrrolate,

oxitropium, oxybutynin, promethazine, propantheline bromide, scopolamine, solifenacin, tolterodine,

tiotropium, trihexyphenidyl, tropicamide, tubecurarine,

mecamylamine, hexamethonium, doxacurionian, dextromethium);

Acetylcholinesterase inhibitors (eg,

physostigmine, neostigmine, pyridostigmine, ambenonium,

demecay, rivastigmine, phenanthrene derivatives,

galantamine, reversible non-competitive alpha-pinene,

piperidines, donepezil, tacrine, edrophyllium, huperemzine,

lucothiamide, lucothiamide); Adenosine receptor antagonists (for example theophylline and theobromine);

Adrenergic receptor antagonists (eg,

phentolamine, phenoxybenzamine, propranolol, Nebivilol,

Atenolol, Oxprenolol, Metoprolol, Timolol, Pindolol,

Nadolol, Pindolol, Esmolol, Acebutolol, Sotalol, Talinolol,

Betaxolol, Labetalol and Carvedalol); Angiotensin receptor antagonists (eg, candesartan, eprosartan,

irbesartan, losartan, olmesartan, telmisartan,

valsartan); Apoptosis stimulants (e.g. asian acid, gluco-oxicoic acid); Cyclo-inhibitors

oxygenase (for example celecoxib, rofecoxib); Inhibitors of cytokine production (eg sirolimus,

basiliximab, daclizumab); Dehydrogenase Inhibitors

((for example mycophenolate mofetil, mycophenolic acid);

Dopamine receptor antagonists (eg,

benperidol, chlorpromazine, clopentixol, droperidol,

haloperidol, fluphenazine, flupentixol, fluspirylene,

penfluridol, perazine, perphenazine, pimozide, spiperone,

sulpiride, thioridazine, amisulpride, aseanapine,

aripriprazole, clozapine, loxapine, nemonapride, olanzapine,

quetiapine, paliperidone, remoxipride, risperidone,

tiapride, ziprasidone, domperidone, bromopride,

metoclopramide, eticlopride, nafadida; EGFR Inhibitors

(eg gefitinib, erlotinib, iapatinib,

osimertinib, cetuximab, neratinib, pnaitumumab,

vandetanib, necitumumab, dacomitinib); ERK1 and ERK2 phosphorylation inhibitors (eg RAF inhibitors,

RAS or MEK); Estrogen receptor agonists (eg ethinylestradiol, diethylstilbestrol,

phytoestrogens, tamoxifen, clomiphene, raloxifene);

Glutamate receptor antagonists (eg AP5,

barbiturates, dextromethorphan, dextrorphan, dizoclipin,

ibogaine, ifenprodil, ketamine, kynurenic acid, memantine,

perampanel, phencyclidine); Histamine receptor antagonists (eg cimetidine, ranitidine, famotidine,

nizatidine, roxatidine, lafutidine); Histone lysine methyltransferase inhibitors (EPZ004777, EPZ5676, BIX01294);

IKK inhibitors (eg, curcumin, embelin,

auranofine, butein, IMD 0354, IKK 16, SC514, BAY 11-7082,

MRT67307, BMS-345541, amlexanox, MLN120B); Ion channel antagonists (eg, erastine); Leucine-rich repeat kinase inhibitors (eg, MLi-2, PF-

06447475, GSK2578215, LRKK2-IN1, HG 10/102/01, CZC-25146);

MDM inhibitors (eg tenovin-2, idasanutlin,

SP141 MI-773, RO8994, AMG232, nutlin-3); Monoamine oxidase inhibitors (eg hydrazine, isocarboxazide,

nialamide, phenelzine, hydracarbazine, trirylcypromine,

befemelan, moclobemide, pirlindol, toloxatone, rasagiline,

selegiline, safinamide); Nucleophosmin inhibitors (eg EAPB0503, NSC348884, Rev37-47 CIGB-300,

avrainvillamide, deguelin, EPTG, YTR107); PPAR receptor agonists (eg, clofibrate, gemfibrozil,

ciprofibrate, bezafibrate, fenofibrate, thiazolidinediones,

BW501516, aleglitazar, muraglitize, tesaglitzar);

Phosphodiesterase inhibitors (eg vinpocetine,

ENHA, BAY 60-7550, oxindole, PDP, IBMX, aminophylline,

praxanthine, pentoxifylline, theobromine, inamrinone,

milrinone, enoximona, anagrelide, cilostazol, pimobendan);

SIRT inhibitors (eg (s)-2-phenyl-6-chloro, 8-

bromo-chroman-4-one, 3'-phenethyloxy-2-anilinobenzamide);

Sodium channel blockers (eg, procainamide,

quinidine, disopyramide, lidocaine, mexiletine, tocainide,

phenytoin, encainide, flecainide, moricizine, propafenone);

and Vitamin D receptor agonists (eg, EB 1089,

BXL-01-0029, elocalcitol). In some embodiments, antiproliferative drugs without anti-inflammatory activity in any context described herein may include JAK inhibitors, JNK inhibitors,

AKT, protein kinase inhibitors, RNA polymerase inhibitors, HSP inhibitors, DNA protein kinase inhibitors, focal adhesion inhibitors, RNA synthesis inhibitors and mediator release inhibitors.

[0145] As used herein, the term "anti-inflammatory" refers to a compound capable of reducing or inhibiting inflammation, where this is the primary activity of the compound in the relevant context. As used herein, the term "anti-inflammatory drug" or "anti-inflammatory agent" is used to describe any compound (including analogs, derivatives, prodrugs and pharmaceutically acceptable salts thereof) that can be used to reduce or inhibit inflammation. Non-limiting examples of anti-inflammatory drugs may include inhibitors of the NFB pathway (eg, 9-methyl-5H-6-thia-4,5-diaza-chrysene-6,6-dioxide, denosumab, disulfiram, olmesartan , dithiocarbamates, anatabine, BAY 11-7082, palmitoylethanolamide, iguartimode); protein synthesis inhibitors (for example chloramphenicol); anti-IL1B antibodies (for example, Canakinumab); glucocorticoid receptor agonists (for example, dexamethasone, mifepristone); and TGF receptor beta inhibitors (for example, LY-364947, GW-755.55, LY-2109761, galunisertibe, SB431542, SB-525334).

Other non-limiting examples of antiproliferative drugs include Acetylcholine receptor antagonists; Acetylcholinesterase inhibitors; Adenosine receptor antagonists; Adrenergic receptor antagonists; Angiotensin receptor antagonists; Apoptosis stimulants; Cyclooxygenase inhibitors; Inhibitors of cytokine production; Dehydrogenase Inhibitors; Dopamine receptor antagonists; EGFR Inhibitors; ERK1 and ERK2 phosphorylation inhibitors; Estrogen receptor agonists; Glutamate receptor antagonists; Histamine Receptor Antagonists; Histone Lysine Methyltransferase Inhibitors; IKK inhibitors; Ion channel antagonists; Leucine-rich repeat kinase inhibitors; MDM Inhibitors; Monoamine oxidase inhibitors; Nucleophosmin Inhibitors; PPAR receptor agonists; Phosphodiesterase Inhibitors; SIRT Inhibitors; Sodium channel blockers; and Vitamin D receptor agonists. In some embodiments, anti-inflammatory drugs lacking antiproliferative activity in any context described herein may include inhibitors of protein synthesis and inhibitors of the TGF beta receptor.

[0146] It should be noted in this document that a single compound may exhibit multiple activities, eg depending on context. Non-limiting examples of agents that may exhibit primarily anti-cancer activity.

inflammatory and/or an antiproliferative activity,

depending on the context (eg the individual or cell being administered/contacted with the agent) may include acetylcholine receptor antagonists, acetylcholinesterase inhibitors, adenosine receptor antagonists, adrenergic receptor antagonists,

angiotensin receptor antagonists, apoptosis stimulants, aurora kinase inhibitors, cdk inhibitors,

cyclooxygenase inhibitors, cytokine production inhibitors, dehydrogenase inhibitors, dopamine receptor antagonists, EGFR inhibitors, ERK1 and ERK2 phosphorylation inhibitors, estrogen receptor agonists, FLT3 inhibitors, glucocorticoid receptor agonists, antagonists of the glutamate receptor,

HDAC inhibitors, histamine receptor antagonists,

histone lysine methyltransferase inhibitors,

HSP, IKK inhibitors, ion channel antagonists,

KIT inhibitors, leucine-rich repeat kinase inhibitors, MEK inhibitors, MDM inhibitors, monoamine oxidase inhibitors, MTOR inhibitors, NFB pathway inhibitors, nucleophosmin inhibitors, PARP inhibitors,

PI3K inhibitors, PPAR receptor agonist,

RAF, SIRT inhibitors, sodium channel blockers,

Topoisomerase inhibitors, tyrosine kinase inhibitors, VEGFR inhibitors and vitamin D receptor agonists.

[0147] An immunostimulating drug is a drug that increases the activity of the immune system, preferably against cancerous or dysplastic cells, where this is the primary activity of the compound in the relevant context. As used herein, the term "immunostimulating drug" or "anti-inflammatory agent" is used to describe any compound (including analogues, derivatives, prodrugs and pharmaceutically acceptable salts thereof) that can be used to stimulate the immune system. . Non-limiting examples of immunostimulating drugs may include immune checkpoint inhibitors (for example, inhibitors against PD-1, PD-L1, CTLA4 and LAG3); drugs that stimulate interferon signaling (for example, antiviral drugs that improve interferon signaling such as Pegintron, Pegasys, Referon A, Uniferon, Multiferon, Rebif, Avonex, Cinnovex, Betaseron, Actimmune, Reiferon, Pegetron); DNA synthesis inhibitors (eg, TAS-102, NC-6004, ganciclovir); CDK inhibitors (for example, purvalanol-a, palbociclib, ribociclib, abemaciclib and olomoucin II); Ribonucleotide reductase inhibitors (for example, motexafine, hydroxyurea, fludarabine, cladribine, gemcitabine, tezacitabine, triapine, gallium maltolate, gallium nitrate); Dihydrofolate reductase inhibitors (eg.

methotrexate, pyritrexam, cycloguanil, JPC-2056); Topoisomerase inhibitors (eg, pydorubicin, doxorubicin,

campothecins, indenosioquinolines, indotecan,

imdimitecan, ansacrine, etoposide, teniposide, ICRF-193,

genistein); FLT3 inhibitors (eg, lestaurtinib,

TG-101348, gilteritinib, quizartinib, midostaurin,

sorafenib, sunitinib); IGF-1 Inhibitors; Inhibitors of

MEK (eg trametinib, cobimetinib, binimetinib,

selumetinib, PD-325901, TAK-733); Kinase Inhibitors

Aurora (for example ZM447439, hesperidin, VX-680);

PKC inhibitors (eg, ruboxistaurine,

chelerythrine, myiabenol C, myricitrine, gossypol,

verbascoside, BIM-1, bryostat 1, tamoxifen); RAF inhibitors (eg, vemurafenib, GDC-0879, PLX-4720,

sorafenib, dabrafenib, LGX818); PDFGR/KIT Inhibitors

(eg imatinib, sunitinib, sorafenib, pazopanib,

nilotinib, motesanib, linifenib); VEGFR Inhibitors

(eg axitinib, cabozantinib, lenvatinib,

pazopanib, vandetanib); SRC inhibitors (for example,

KX2-391, bosutinib, saracatinib, PP1, PP2, quercetin,

dastabinib); Retinoid receptor agonists (eg, alitretinoin, isoretinoin); HDAC inhibitors

(for example, THM-I-94, vorinostat, givinostat);

DNA methyltransferase inhibitors (for example azacitidine, decitabine, zeublarin); and EZH2 Inhibitors (DZNep, EPZ005687, EI1, GSK126, UNC1999, EPZ-6438, tazemetostat).

[0148] In some embodiments, immune stimulant drugs lacking antiproliferative/inflammatory activity in any context described herein may include immune checkpoint inhibitors (eg, inhibitors against PD-1, PD-L1, CTLA4, and LAG3); drugs that stimulate interferon signaling (eg, antiviral drugs that improve interferon signaling); DNA synthesis inhibitors; IMDH inhibitors; ribonucleotide reductase inhibitors; Dihydrofolate reductase inhibitors; SRC inhibitors; Retinoid receptor agonists; HDAC inhibitors; and DNA methyltransferase inhibitors.

[0149] The term "effective amount", as used herein, refers to the amount of a composition necessary to alleviate at least one or more symptoms of the disease or disorder and refers to a sufficient amount of pharmaceutical composition to confer the effect wanted.

The term "therapeutically effective amount", therefore, refers to an amount of the composition that is sufficient to impart a particular therapeutic effect when administered to a typical individual. An effective amount, as used herein in various contexts, would also include an amount sufficient to delay the development of a disease symptom, alter the course of a disease symptom (eg, but not limited to, delay the progression of a symptom disease) or reversing a symptom of the disease. Thus, in general, it is not practicable to specify an exact "effective amount". However, in any case, an appropriate "effective amount" can be determined by those skilled in the art using only routine experimentation.

[0150] Effective amounts, toxicity and therapeutic efficacy can be determined by standard pharmaceutical procedures in cell cultures or experimental animals, for example, to determine the LD50 (the dose lethal to 50% of the population) and the ED50 (the dose therapeutically effective in 50% of the population). The dosage may vary depending on the dosage form employed and the route of administration used. The dose ratio between toxic and therapeutic effects is the therapeutic index and can be expressed as the LD50/ED50 ratio. Compositions and methods that exhibit large therapeutic indices are preferred. A therapeutically effective dose can be estimated initially from cell culture assays. In addition, a dose can be formulated in animal models to achieve a circulating plasma concentration range that includes the IC50 (ie, the concentration of active ingredient that achieves half the maximum inhibition of symptoms) as determined in cell culture or in an appropriate animal model. Plasma levels can be measured, for example, by high performance liquid chromatography. The effects of any particular dosage can be monitored through a suitable bioassay, eg, gene expression assay as described herein, among others. Dosage can be determined by a physician and adjusted as needed to suit the observed effects of treatment.

[0151] In some embodiments, the technology described herein refers to a pharmaceutical composition comprising a drug as described herein and, optionally, a pharmaceutically acceptable carrier. In some embodiments, the active ingredients of the pharmaceutical composition comprise the drug as described herein. In some embodiments, the active ingredients of the pharmaceutical composition consist essentially of the drug as described herein. In some embodiments, the active ingredients of the pharmaceutical composition are the drug as described herein. Pharmaceutically acceptable carriers and diluents include saline, aqueous buffer solutions, solvents and/or dispersion media.

The use of such carriers and diluents is well known in the art. Some non-limiting examples of materials that can serve as pharmaceutically acceptable carriers include: (1) sugars, such as lactose, glucose and sucrose; (2) starches such as corn starch and potato starch; (3) cellulose and derivatives thereof, such as sodium carboxymethylcellulose, methylcellulose, ethylcellulose, microcrystalline cellulose and cellulose acetate; (4) powdered tragacanth; (5) malt; (6) gelatin; (7) lubricating agents such as magnesium stearate, sodium lauryl sulfate and talc; (8) excipients such as cocoa butter and suppository waxes; (9) oils, such as peanut oil, cottonseed oil, safflower oil, sesame oil, olive oil, corn oil and soybean oil; (10) glycols, such as propylene glycol; (11) polyols such as glycerin, sorbitol, mannitol and polyethylene glycol (PEG); (12) esters, such as ethyl oleate and ethyl laurate; (13) agar; (14) buffering agents such as magnesium hydroxide and aluminum hydroxide; (15) alginic acid; (16) pyrogenic water; (17) isotonic saline solution; (18) Ringer's solution; (19) ethyl alcohol; (20)

buffered pH solutions; (21) polyesters, polycarbonates and/or polyanhydrides; (22) bulking agents such as polypeptides and amino acids; (23) serum components such as serum albumin, HDL and LDL; (24) C2-C12 alcohols, such as ethanol; and (25) other compatible non-toxic substances used in pharmaceutical formulations. Wetting agents, coloring agents, release agents, coating agents, sweetening agents, flavoring agents, flavoring agents, preservatives and antioxidants may also be present in the formulation. Terms such as "excipient", "carrier", "pharmaceutically acceptable carrier" or the like are used interchangeably herein. In some modalities, the carrier inhibits the degradation of the active agent.

[0152] In some embodiments, the pharmaceutical composition comprising a drug as described herein can be a parenteral dosage form.

Since administration of parenteral dosage forms typically bypasses the patient's natural defenses against contaminants, parenteral dosage forms are preferably sterile or capable of being sterilized prior to administration to a patient. Examples of parenteral dosage forms include, but are not limited to, injection-ready solutions, dry products ready to be dissolved or suspended in a pharmaceutically acceptable vehicle for injection, injection-ready suspensions, and emulsions. In addition, controlled release parenteral dosage forms can be prepared for administration to a patient including, but not limited to, HARD and dumping dosage forms.

Suitable vehicles that can be used to deliver parenteral dosage forms of a drug as described are well known to those skilled in the art. Examples include, without limitation: sterile water; water for injectables USP; saline solution; glucose solution; aqueous vehicles such as, but not limited to, Sodium Chloride Injection, Ringer's Injection, Dextrose Injection, Dextrose and Sodium Chloride Injection, and Lactated Ringer's Injection; water miscible vehicles such as, but not limited to, ethyl alcohol, polyethylene glycol and propylene glycol; and non-aqueous vehicles such as, but not limited to, corn oil, cottonseed oil, peanut oil, sesame oil, ethyl oleate, isopropyl myristate and benzyl benzoate. Compounds that alter or modify the solubility of a pharmaceutically acceptable salt of the drug, as described herein, may also be incorporated into the parenteral dosage forms of the invention, including conventional and controlled-release parenteral dosage forms.

[0154] Pharmaceutical compositions comprising a drug may also be formulated so as to be suitable for oral administration, for example, as distinct dosage forms such as, but not limited to, tablets (including, without limitation, marked or coated tablets) , pills, small capsules, capsules, chewable tablets, powder packets, wafers, troches, wafers, aerosol sprays or liquids such as, but not limited to, syrups, elixirs, solutions or suspensions in an aqueous liquid, a non-aqueous liquid, an oil-in-water emulsion or a water-in-oil emulsion. Such compositions contain a predetermined amount of the pharmaceutically acceptable salt of the described compounds and can be prepared by pharmaceutical methods well known to those skilled in the art. See, generally, Remington: The Science and Practice of Pharmacy, 21st Ed., Lippincott, Williams and Wilkins, Philadelphia PA. (2005).

[0155] Conventional dosage forms generally allow for quick or immediate release of the drug from the formulation. Depending on the pharmacology and pharmacokinetics of the drug, the use of conventional dosage forms can lead to large fluctuations in drug concentrations in the patient's blood and other tissues. These fluctuations can have an impact on a number of parameters, such as dose frequency, onset of action, duration of efficacy, maintenance of therapeutic blood levels, toxicity, side effects, and so on. Advantageously, controlled release formulations can be used to control the onset of action of a drug, duration of action, plasma levels within the therapeutic window, and peak blood levels.

In particular, controlled or sustained release dosage forms or formulations can be used to ensure that the maximum efficacy of a drug is achieved, minimizing the potential adverse effects and safety concerns that can occur both from underdosing of a drug. (ie, going below minimal therapeutic levels) as well as exceeding the drug's toxicity level. In some modalities, the drug can be administered in a sustained-release formulation.

[0156] Controlled-release pharmaceuticals have a common goal of improving drug therapy over that achieved by their non-controlled-release counterparts. Ideally, the use of an ideally designed controlled release preparation for medical treatment is characterized by a minimum of drug substance being employed to cure or control the condition in a minimum period of time. The advantages of controlled-release formulations include: 1) prolonged drug activity; 2) reduced dosing frequency; 3) increased patient compliance; 4) use of less total drug; 5) reduction of local or systemic side effects; 6) minimization of drug accumulation; 7) reduced fluctuations in blood levels; 8) improved treatment effectiveness; 9) reduced potentiation or loss of drug activity; and 10) improved speed of disease or condition control. Kim, Cherng-ju, Controlled Release Dosage Form Design, 2 (Technomic Publishing, Lancaster, Pa.: 2000).

[0157] Most controlled-release formulations are designed to initially release an amount of drug (active ingredient) that readily produces the desired therapeutic effect and gradually and continuously release other amounts of drug to maintain this level of therapeutic or prophylactic effect during a extended period of time. In order to maintain this constant level of drug in the body, the drug must be released from the dosage form at a rate that will replenish the amount of drug being metabolized and excreted from the body. Controlled release of an active ingredient can be stimulated by various conditions including, but not limited to, pH, ionic strength, osmotic pressure, temperature, enzymes, water, and other physiological conditions or compounds.

[0158] A variety of controlled or sustained release dosage forms, formulations and devices can be adapted for use with the salts and compositions of the invention.

Examples include, but are not limited to, those described in U.S. Patent Nos. 3,845,770; 3,916,899; 3,536,809; 3,598,123; 4,008,719; 5,674,533; 5,059,595; 5,591.767; 5,120,548; 5,073,543; 5,639,476; 5,354,556; 5,733,566; and 6,365,185 B1; each of which is incorporated herein by reference. These dosage forms can be used to allow slow or controlled release of one or more active ingredients using, for example, hydroxypropylmethylcellulose, other polymeric matrices, gels, permeable membranes, osmotic systems (such as OROS® (Alza Corporation, Mountain View, California, USA)) or a combination thereof to provide the desired release profile in varying proportions.

[0159] In some embodiments of either aspect, the drug described herein is administered as a monotherapy, for example, another treatment for bronchial premalignant lesions is not administered to the individual.

[0160] In some embodiments of either aspect, the methods described herein may further comprise administering a second agent and/or treatment to the individual, for example, as part of a combination therapy.

[0161] In certain embodiments, an effective dose of a composition comprising a drug as described herein may be administered to a patient one time. In certain embodiments, an effective dose of a composition comprising a drug can be administered to a patient repeatedly. For systemic administration, subjects may receive a therapeutic amount of a composition comprising a drug such as, for example, 0.1 mg/kg, 0.5 mg/kg, 1.0 mg/kg, 2.0 mg/ kg, 2.5 mg/kg, 5 mg/kg, 10 mg/kg, 15 mg/kg, 20 mg/kg, 25 mg/kg, 30 mg/kg, 40 mg/kg, 50 mg/kg or more .

[0162] In some modalities, after an initial treatment regimen, treatments may be given less frequently. For example, after biweekly treatment for three months, the treatment can be repeated once a month, for six months or a year or more. Treatment according to the methods described herein can reduce the levels of a marker or symptom of a condition, for example, by at least 10%, at least 15%, at least 20%, at least 25%, at least 30%, at least 40%, at least 50%, at least 60%, at least 70%, at least 80% or at least 90% or more.

[0163] The dosage of a composition as described herein can be determined by a physician and adjusted, as necessary, to suit the observed effects of treatment. With regard to the duration and frequency of treatment, it is typical for qualified physicians to monitor individuals in order to determine when the treatment is providing a therapeutic benefit and to determine whether to increase or decrease the dosage, increase or decrease the frequency of administration, discontinue the treatment, resume treatment or make other changes to the treatment regimen. The dosage schedule can vary from once a week to daily, depending on a number of clinical factors, such as the individual's sensitivity to the active ingredient. The desired dose or amount of activation may be administered all at once or divided into subdoses, for example 2-4 subdoses, and administered over a period of time, for example, at appropriate intervals throughout the day or other appropriate schedule. In some modalities, the administration can be chronic, for example,

one or more daily doses and/or treatments over a period of weeks or months. Examples of dosage and/or treatment schedules are administration daily, twice a day, three times a day or four or more times a day for a period of 1 week, 2 weeks, 3 weeks, 4 weeks, 1 month, 2 months , 3 months, 4 months, 5 months or 6 months or more. A composition comprising a drug described herein may be administered over a period of time, such as over a period of 5 minutes, 10 minutes, 15 minutes, 20 minutes or 25 minutes.

[0164] The dosage intervals for the administration of a drug, according to the methods described in this document depend, for example, on the form of the drug, its potency and to what extent it is desired that the symptoms, markers or indicators of a condition described in this document are to be reduced, for example, the desired percentage reduction for the size of the lesion or the extent to which, for example, it is desired to induce changes in the lesion subtype. The dosage should not be so great as to cause adverse side effects. In general, the dosage will vary with the age, condition and sex of the patient and can be determined by those skilled in the art. The dosage can also be adjusted by the individual doctor in case of any complications.

[0165] The effectiveness of a drug, for example, in treating a condition described herein or to induce a response as described herein (for example, reduction in lesion size) can be determined by the specialist physician. However, a treatment is considered "effective treatment" as the term is used herein, if one or more of the signs or symptoms of a condition described herein are beneficially altered, other clinically accepted symptoms are ameliorated, or even relieved, or a desired response is induced, for example, by at least 10% after treatment according to the methods described herein. Efficacy can be assessed, for example, by measuring a marker, indicator, symptom and/or incidence of a condition treated according to the methods described herein or any other appropriate measurable parameter. Efficacy can also be measured by the absence of a worsening in the individual, as assessed by hospitalization or need for medical intervention (ie, disease progression is halted). Methods for measuring these indicators are known to those skilled in the art and/or are described herein.

Treatment includes any treatment of a disease in an individual or animal (some non-limiting examples include a human or an animal) and includes: (1) inhibiting the disease, e.g., preventing worsening of symptoms (eg, pain or inflammation); or (2) alleviating the severity of the illness, for example, causing the regression of symptoms. An effective amount for treating a disease means that amount which, when administered to an individual in need thereof, is sufficient to result in an effective treatment as this term is defined herein for that disease. An agent's effectiveness can be determined by evaluating physical indicators of a desired condition or response. It is well within the ability of those skilled in the art to monitor the effectiveness of administration and/or treatment by measuring any such parameter or any combination of parameters. Efficacy can be evaluated in animal models of a condition described herein, for example, the treatment of pre-malignant bronchial lesions in a mouse model. When using an experimental animal model, the effectiveness of the treatment is evidenced when a statistically significant change in a marker is observed, for example, lesion size or gene expression.

[0166] As used herein, "a bronchoscopy-based procedure" refers to any endoscopic technique that allows examination of the bronchi and/or lungs. Bronchoscopy-based procedures may include white-light bronchoscopy, autofluorescent bronchoscopy, flexible bronchoscopy, rigid bronchoscopy, bronchoalveolar lavage, and so on. Bronchoscopy-based procedures may include biopsy, smear, or tissue sampling.

[0167] In addition to treatment methods, the methods and biomarker signatures described herein can be applied to methods of predicting lung cancer risk in an individual and/or determining treatment efficacy or need for further treatment. For example, transitioning from a Proliferative or Inflammatory subtype to a Normal or Secretor subtype would indicate that a treatment was effective or that the treatment can be discontinued.

[0168] In one aspect of any of the embodiments, a method of predicting the risk or likelihood of progression to lung cancer in an individual is described herein, the method comprising: detecting the expression level of at least one gene from module 5 and/or at least one gene from module 6 in a sample obtained from the subject, wherein an increased expression level of at least one gene from module 5 compared to a reference level of non-proliferative lesion; and/or a reduced expression level of at least one module 6 gene compared to a reference level of non-proliferative lesion indicates an increased risk or likelihood of progressing to lung cancer.

In one aspect of either mode. Described herein is a method of predicting the risk or probability of progression to lung cancer in an individual, the method comprising: detecting the expression level of at least one module 5 gene and/or at least one module gene 6 in a sample obtained from the individual at a first time point and detecting the expression level of at least one gene from module 5 and/or at least one gene from module 6 in a sample obtained from the individual at a second subsequent time point , in which an increased expression level of at least one module 5 gene over time; and/or a reduced expression level of at least one module 6 gene over time indicates an increased risk or likelihood of progressing to lung cancer.

[0169] In one aspect of any of the embodiments, a method of predicting the risk or likelihood of progression to lung cancer in an individual is described herein, the method comprising: detecting the expression level of at least one gene from module 9 and/or at least one gene from module 10 in a sample obtained from the subject, wherein an increased expression level of at least one gene from module 10 compared to a reference level of non-proliferative lesion; and/or a reduced expression level of at least one module 9 gene compared to a reference level of non-proliferative lesion indicates an increased risk or likelihood of progressing to lung cancer.

In one aspect of either embodiment, a method of predicting the risk or likelihood of progression to lung cancer in an individual is described herein, the method comprising: detecting the expression level of at least one module 10 gene. and/or at least one module 9 gene in a sample obtained from the subject at a first time point and detecting the expression level of at least one module 9 gene and/or at least one module 10 gene in an obtained sample of the individual at a second subsequent time point, where an expression level of at least one module 10 gene increases over time; and/or a reduced expression level of at least one module 9 gene over time indicates an increased risk or likelihood of progressing to lung cancer.

[0170] In one aspect of any of the embodiments, a method of predicting the risk or likelihood of progression to lung cancer in an individual is described herein, the method comprising: detecting the expression level of at least one gene from module 2 and/or at least one gene from module 6 in a sample obtained from the subject, wherein an increased expression level of at least one gene from module 2 compared to a reference level of non-proliferative lesion; and/or a reduced expression level of at least one module 6 gene compared to a reference level of non-proliferative lesion indicates an increased risk or likelihood of progressing to lung cancer.

In one aspect of either embodiment, a method of predicting the risk or likelihood of progression to lung cancer in an individual is described herein, the method comprising: detecting the expression level of at least one module 2 gene and/or at least one module 6 gene in a sample obtained from the individual at a first time point and detecting the expression level of at least one module 2 gene and/or at least one module 6 gene in an obtained sample of the individual at a second subsequent time point, in which an increased expression level of at least one module 2 gene over time; and/or a reduced expression level of at least one module 6 gene over time indicates an increased risk or likelihood of progressing to lung cancer.

[0171] In an aspect of any of the embodiments, a method for determining the effectiveness of treatment is described herein, the method comprising: detecting the expression level of at least one module 5 gene and/or at least one gene of module 6 in a sample obtained from the subject at a first time point, administering a candidate treatment or treatment and detecting the expression level of at least one module 5 gene and/or at least one module 6 gene in an obtained sample of the individual at a second subsequent time point, where a reduced expression level of at least one module 5 gene over time; and/or an increased expression level of at least one module 6 gene over time indicates that the treatment is effective.

[0172] In one aspect of any of the embodiments, a method for evaluating the effectiveness of a treatment is described herein, the method comprising: detecting the expression level of at least one module 10 gene and/or at least one modulo 9 gene in a sample obtained from the subject at a first time point, administering a candidate treatment or treatment and detecting the expression level of at least one modulo 9 gene and/or at least one modulo 10 gene in a sample obtained from the individual at a second subsequent time point, where a reduced expression level of at least one module 10 gene over time; and/or an increased expression level of at least one module 9 gene over time indicates that the treatment is effective.

[0173] In one aspect of any of the embodiments, a method for determining the effectiveness of treatment is described herein, the method comprising: detecting the expression level of at least one module 2 gene and/or at least one gene of module 6 in a sample obtained from the subject at a first time point, administer a candidate treatment or treatment and detect the expression level of at least one module 2 gene and/or at least one module 6 gene in an obtained sample of the individual at a second subsequent time point, where a reduced expression level of at least one module 2 gene over time; and/or an increased expression level of at least one module 6 gene over time indicates that the treatment is effective.

[0174] In an aspect of any of the embodiments, a method is described herein comprising: detecting the expression level of at least one module 5 gene and/or at least one module 6 gene in a sample obtained from an individual, in which the expression level of no more than 1,000 (for example, no more than 500, 400, 300, 200 or 100) genes is determined. In one aspect of either embodiment, a method is described herein comprising: detecting the level of expression of at least one module 9 gene and/or at least one module 10 gene in a sample obtained from an individual, where the expression level of no more than 1,000 (for example, no more than 500, 400, 300, 200, or 100) genes is determined. In one aspect of any of the embodiments, described herein is a method comprising: detecting the level of expression of at least one module 2 gene and/or at least one module 6 gene in a sample obtained from an individual, wherein the expression level of no more than 1,000 (for example, no more than 500, 400, 300, 200, or 100) genes is determined. In some modalities of either aspect, the specimen is a bronchial smear specimen. In some embodiments of either aspect, at least one of the gene is selected from Table 14 or 15.

Table 13 EnsemblID Genetic Module Gene Symbols 1 ENSG00000001084 GCLC 1 ENSG00000006210 CX3CL1 1 ENSG00000008256 CYTH3 1 ENSG00000010319 SEMA3G 1 ENSG00000011028 MRC2 1 ENSG00000011201 KAL1

1 ENSG00000011523 CEP68

1 ENSG00000012660 ELOVL5

1 ENSG00000017483 SLC38A5

1 ENSG00000019144 PHLDB1

1 ENSG00000019549 SNAI2

1 ENSG00000020181 GPR124

1 ENSG00000020577 SAMD4A

1 ENSG00000024422 EHD2

1 ENSG00000031081 ARHGAP31

1 ENSG00000035862 TIMP2

1 ENSG00000042832 TG

1 ENSG00000049130 KITLG

1 ENSG00000049540 ELN

1 ENSG00000050165 DKK3

1 ENSG00000053747 MUD3

1 ENSG00000054965 FAM168A

1 ENSG00000060140 STYK1

1 ENSG00000061918 GUCY1B3

1 ENSG00000063180 CA11

1 ENSG00000064042 LIMCH1

1 ENSG00000064205 WISP2

1 ENSG00000064300 NGFR

1 ENSG00000064989 CALCRL

1 ENSG00000065054 SLC9A3R2

1 ENSG00000065320 NTN1

1 ENSG00000067445 TRO

1 ENSG00000069122 GPR116

1 ENSG00000069188 SDK2

1 ENSG00000069702 TGFBR3

1 ENSG00000071246 VASH1

1 ENSG00000072041 SLC6A15

1 ENSG00000072195 SPEG

1 ENSG00000072210 ALDH3A2

1 ENSG00000072840 EVC

1 ENSG00000073067 CYP2W1

1 ENSG00000073282 TP63

1 ENSG00000073712 FERMT2

1 ENSG00000074356 C17orf85

1 ENSG00000074590 NUAK1

1 ENSG00000074660 SCARF1

1 ENSG00000076706 MCAM

1 ENSG00000077782 FGFR1

1 ENSG00000078018 MAP2

1 ENSG00000079102 RUNX1T1

1 ENSG00000079308 TNS1

1 ENSG00000080573 COL5A3

1 ENSG00000081052 COL4A4

1 ENSG00000081913 PHLPP1

1 ENSG00000082497 SERTAD4

1 ENSG00000082781 ITGB5

1 ENSG00000085998 POMGNT1

1 ENSG00000087116 ADAMTS2

1 ENSG00000087245 MMP2

1 ENSG00000088367 EPB41L1

1 ENSG00000091136 LAMB1

1 ENSG00000091879 ANGPT2

1 ENSG00000092096 SLC22A17

1 ENSG00000092421 WEEK6A

1 ENSG00000092969 TGFB2

1 ENSG00000099953 MMP11

1 ENSG00000100154 TTC28

1 ENSG00000101331 CCM2L

1 ENSG00000101665 SMAD7

1 ENSG00000101825 MXRA5

1 ENSG00000102302 FGD1

1 ENSG00000102755 FLT1

1 ENSG00000103196 CRISPLD2

1 ENSG00000103241 FOXF1

1 ENSG00000103723 AP3B2

1 ENSG00000103852 TTC23

1 ENSG00000104953 TLE6

1 ENSG00000105088 OLFM2

1 ENSG00000105227 PRX

1 ENSG00000105371 ICAM4

1 ENSG00000105376 ICAM5

1 ENSG00000105419 MEIS3

1 ENSG00000105538 RASIP1

1 ENSG00000105738 SIPA1L3

1 ENSG00000105866 SP4

1 ENSG00000105974 CAV1

1 ENSG00000106070 GRB10

1 ENSG00000106123 EPHB6

1 ENSG00000106333 PCOLCE

1 ENSG00000106571 GLI3

1 ENSG00000106624 AEBP1

1 ENSG00000108821 COL1A1

1 ENSG00000108852 MPP2

1 ENSG00000108924 HLF

1 ENSG00000109099 PMP22

1 ENSG00000109107 ALDOC

1 ENSG00000109193 SULT1E1

1 ENSG00000109610 SOD3

1 ENSG00000110002 VWA5A

1 ENSG00000110200 ANAPC15

1 ENSG00000110799 VWF

1 ENSG00000110811 LEPREL2

1 ENSG00000111341 MGP

1 ENSG00000111452 GPR133

1 ENSG00000111799 COL12A1

1 ENSG00000112320 SOBP

1 ENSG00000112414 GPR126

1 ENSG00000112562 SMOC2

1 ENSG00000112769 MUD4

1 ENSG00000112782 CLIC5

1 ENSG00000112902 WEEK5A

1 ENSG00000112936 C7

1 ENSG00000112964 GHR

1 ENSG00000113140 SPARC

1 ENSG00000113555 PCDH12

1 ENSG00000114270 COL7A1

1 ENSG00000114698 PLSCR4

1 ENSG00000114923 SLC4A3

1 ENSG00000115252 PDE1A

1 ENSG00000115306 SPTBN1

1 ENSG00000115380 EFEMP1

1 ENSG00000115414 FN1

1 ENSG00000116016 EPAS1

1 ENSG00000116678 LEPR

1 ENSG00000116774 OLFML3

1 ENSG00000116962 NID1

1 ENSG00000117013 KCNQ4

1 ENSG00000117122 MFAP2

1 ENSG00000117385 LEPRE1

1 ENSG00000117643 MAN1C1

1 ENSG00000118495 PLAGL1

1 ENSG00000119138 KLF9

1 ENSG00000119681 LTBP2

1 ENSG00000119699 TGFB3

1 ENSG00000119771 KLHL29

1 ENSG00000120156 TEK

1 ENSG00000120162 MOB3B

1 ENSG00000120318 ARAP3

1 ENSG00000120457 KCNJ5

1 ENSG00000121068 TBX2

1 ENSG00000121075 TBX4

1 ENSG00000122035 RASL11A

1 ENSG00000122642 FKBP9

1 ENSG00000122707 RECK

1 ENSG00000122778 KIAA1549

1 ENSG000001222786 CALD1

1 ENSG00000123094 RASSF8

1 ENSG00000123384 LRP1

1 ENSG00000124006 OBSL1

1 ENSG00000124406 ATP8A1

1 ENSG00000125266 EFNB2

1 ENSG00000125810 CD93

1 ENSG00000125848 FLRT3

1 ENSG00000126803 HSPA2

1 ENSG00000127329 PTPRB

1 ENSG00000127585 FBXL16

1 ENSG00000127920 GNG11

1 ENSG00000127946 HIP1

1 ENSG00000128052 KDR

1 ENSG00000128567 PODXL

1 ENSG00000128641 MYO1B

1 ENSG00000128656 CHN1

1 ENSG00000128791 TWSG1

1 ENSG00000128872 TMOD2

1 ENSG00000128917 DLL4

1 ENSG00000129009 ISLR

1 ENSG00000129038 LOXL1

1 ENSG00000129467 ADCY4

1 ENSG00000129474 AJUBA

1 ENSG00000129946 SHC2

1 ENSG000001299990 SYT5

1 ENSG00000130052 STARD8

1 ENSG00000130300 PLVAP

1 ENSG00000130508 PXDN

1 ENSG00000130635 COL5A1

1 ENSG00000131016 AKAP12

1 ENSG00000131477 RAMP2

1 ENSG00000131831 RAI2

1 ENSG00000132688 NES

1 ENSG00000133026 MYH10

1 ENSG00000133067 LGR6

1 ENSG00000133110 POSTN

1 ENSG00000133121 STARD13

1 ENSG00000133313 CNDP2

1 ENSG00000133687 TMTC1

1 ENSG00000134243 SORT1

1 ENSG00000134245 WNT2B

1 ENSG00000134318 ROCK2

1 ENSG00000134352 IL6ST

1 ENSG00000134569 LRP4

1 ENSG00000134590 FAM127A

1 ENSG00000134627 PIWIL4

1 ENSG00000134802 SLC43A3

1 ENSG00000134853 PDGFRA

1 ENSG00000134917 ADAMTS8

1 ENSG00000134986 NREP

1 ENSG00000135063 FAM189A2

1 ENSG00000135111 TBX3

1 ENSG00000135423 GLS2

1 ENSG00000135424 ITGA7

1 ENSG00000135775 COG2

1 ENSG00000135862 LAMC1

1 ENSG00000135925 WNT10A

1 ENSG00000136114 THSD1

1 ENSG00000136158 SPRY2

1 ENSG00000136160 EDNRB

1 ENSG00000136205 TNS3

1 ENSG00000136274 NACAD

1 ENSG00000136546 SCN7A

1 ENSG00000137273 FOXF2

1 ENSG00000137834 SMAD6

1 ENSG00000137872 SEMA6D

1 ENSG00000137962 ARHGAP29

1 ENSG00000138356 AOX1

1 ENSG00000138495 COX17

1 ENSG00000138735 PDE5A

1 ENSG00000138792 ENPEP

1 ENSG00000138795 LEF1

1 ENSG00000139174 PRICKLE1

1 ENSG00000139211 AMIGO2

1 ENSG00000139263 LRIG3

1 ENSG00000140092 FBLN5

1 ENSG00000140682 TGFB1I1

1 ENSG00000140807 NKD1

1 ENSG00000140937 CDH11

1 ENSG00000141338 ABCA8

1 ENSG00000141622 RNF165

1 ENSG00000141720 PIP4K2B

1 ENSG00000141756 FKBP10

1 ENSG00000142156 COL6A1

1 ENSG00000142173 COL6A2

1 ENSG00000142798 HSPG2

1 ENSG00000143067 ZNF697

1 ENSG00000143140 GJA5

1 ENSG00000143341 HMCN1

1 ENSG00000143995 MEIS1

1 ENSG00000144057 ST6GAL2

1 ENSG00000144642 RBMS3

1 ENSG00000144724 PTPRG

1 ENSG00000144810 COL8A1

1 ENSG00000144857 BOC

1 ENSG00000145040 UCN2

1 ENSG00000145147 SLIT2

1 ENSG00000145675 PIK3R1

1 ENSG00000145777 TSLP

1 ENSG00000146648 EGFR

1 ENSG00000146966 DENND2A

1 ENSG00000147027 TMEM47

1 ENSG00000147257 GPC3

1 ENSG00000147408 CSGALNACT1

1 ENSG00000147862 NFIB

1 ENSG00000148468 FAM171A1

1 ENSG00000148541 FAM13C

1 ENSG00000148600 CDHR1

1 ENSG00000149212 SESN3

1 ENSG00000149294 NCAM1

1 ENSG00000149485 FADS1

1 ENSG00000149564 ESAM

1 ENSG00000149575 SCN2B

1 ENSG00000149582 TMEM25

1 ENSG00000149596 JPH2

1 ENSG00000149639 SOGA1

1 ENSG00000150048 CLEC1A

1 ENSG00000150457 LATS2

1 ENSG00000150471 LPHN3

1 ENSG00000150625 GPM6A

1 ENSG00000150938 CRIM1

1 ENSG00000151617 EDNRA

1 ENSG00000151632 AKR1C2

1 ENSG00000151914 DST

1 ENSG00000152104 PTPN14

1 ENSG00000152217 SETBP1

1 ENSG00000152583 SPARCL1

1 ENSG00000152990 GPR125

1 ENSG00000153162 BMP6

1 ENSG00000153208 MERTK

1 ENSG00000153253 SCN3A

1 ENSG00000153885 KCTD15

1 ENSG00000154065 ANKRD29

1 ENSG00000154122 ANKH

1 ENSG00000154133 ROBO4

1 ENSG00000154188 ANGPT1

1 ENSG00000154310 TNIK

1 ENSG00000154342 WNT3A

1 ENSG00000154358 OBSCN

1 ENSG00000154767 XPC

1 ENSG00000154783 FGD5

1 ENSG00000155254 MARVELD1

1 ENSG00000155324 GRAMD3

1 ENSG00000156011 PSD3

1 ENSG00000156298 TSPAN7

1 ENSG00000156966 B3GNT7

1 ENSG00000157240 FZD1

1 ENSG00000157404 KIT

1 ENSG00000157510 AFAP1L1

1 ENSG00000157554 ERG

1 ENSG00000158270 COLEC12

1 ENSG00000158301 GGRASP2

1 ENSG00000158352 SHROOM4

1 ENSG00000158435 CNOT11

1 ENSG00000159164 SV2A

1 ENSG00000159640 ACE

1 ENSG00000159692 CTBP1

1 ENSG00000160190 SLC37A1

1 ENSG00000160191 PDE9A

1 ENSG00000160469 BRSK1

1 ENSG00000160867 FGFR4

1 ENSG000001161940 BCL6B

1 ENSG00000162367 TAL1

1 ENSG00000162407 PPAP2B

1 ENSG00000162493 PDPN

1 ENSG00000162552 WNT4

1 ENSG00000162576 MXRA8

1 ENSG00000162591 MEGF6

1 ENSG00000162599 NFIA

1 ENSG00000162618 ELTD1

1 ENSG00000162627 SNX7

1 ENSG00000162729 IGSF8

1 ENSG00000162733 DDR2

1 ENSG00000162817 C1orf115

1 ENSG00000163072 NOSTRIN

1 ENSG00000163273 NPPC

1 ENSG00000163328 GPR155

1 ENSG00000163359 COL6A3

1 ENSG00000163378 EOGT

1 ENSG00000163430 FSTL1

1 ENSG00000163435 ELF3

1 ENSG00000163520 FBLN2

1 ENSG00000163710 PCOLCE2

1 ENSG00000163827 LRRC2

1 ENSG00000164056 SPRY1

1 ENSG00000164116 GUCY1A3

1 ENSG00000164176 EDIL3

1 ENSG00000164488 DACT2

1 ENSG00000164692 COL1A2

1 ENSG00000164741 DLC1

1 ENSG00000165125 TRPV6

1 ENSG00000165659 DACH1

1 ENSG00000165757 KIAA1462

1 ENSG00000165821 SALL2

1 ENSG00000165995 CACNB2

1 ENSG00000166025 AMOTL1

1 ENSG00000166086 JAM3

1 ENSG00000166105 GLB1L3

1 ENSG00000166147 FBN1

1 ENSG00000166257 SCN3B

1 ENSG00000166265 CYYR1

1 ENSG00000166292 TMEM100

1 ENSG00000166398 KIAA0355

1 ENSG00000166482 MFAP4

1 ENSG00000166813 KIF7

1 ENSG00000166886 NAB2

1 ENSG00000167123 FENCE

1 ENSG00000168056 LTBP3

1 ENSG00000168060 NAALADL1

1 ENSG00000168077 SCARA3

1 ENSG00000168264 IRF2BP2

1 ENSG00000168490 PHYHIP

1 ENSG00000168497 SDPR

1 ENSG00000168502 SOGA2

1 ENSG00000168542 COL3A1

1 ENSG00000168621 GDNF

1 ENSG00000168818 STX18

1 ENSG00000168890 TMEM150A

1 ENSG00000169047 IRS1

1 ENSG00000169291 SHE

1 ENSG00000169302 STK32A

1 ENSG00000169418 NPR1

1 ENSG00000169435 RASSF6

1 ENSG00000169504 CLIC4

1 ENSG00000169604 ANTXR1

1 ENSG00000169744 LDB2

1 ENSG00000170017 ALCAM

1 ENSG00000170364 SETMAR

1 ENSG00000170549 IRX1

1 ENSG00000170558 CDH2

1 ENSG00000170915 PAQR8

1 ENSG00000171016 PYGO1

1 ENSG00000171033 PKIA

1 ENSG00000171243 SOSTDC1

1 ENSG00000171346 KRT15

1 ENSG00000171444 MCC

1 ENSG00000171462 DLK2

1 ENSG00000171791 BCL2

1 ENSG00000171812 COL8A2

1 ENSG00000171867 PRNP

1 ENSG00000172348 RCAN2

1 ENSG00000172458 IL17D

1 ENSG00000172638 EFEMP2

1 ENSG00000172889 EGFL7

1 ENSG00000173040 EVC2

1 ENSG00000173210 ABLIM3

1 ENSG00000173269 MMRN2

1 ENSG00000173546 CSPG4

1 ENSG00000173706 HEG1

1 ENSG00000173805 HAP1

1 ENSG00000174059 CD34

1 ENSG00000174226 SNX31

1 ENSG00000174348 PODN

1 ENSG00000174370 C11orf45

1 ENSG00000174567 GOLT1A

1 ENSG00000174640 SLCO2A1

1 ENSG00000175471 MCTP1

1 ENSG00000175920 DOK7

1 ENSG00000176393 RNPEP

1 ENSG00000176428 VPS37D

1 ENSG00000176435 CLEC14A

1 ENSG00000176771 NCKAP5

1 ENSG00000176971 FIBIN

1 ENSG00000177076 ACER2

1 ENSG00000177303 CASKIN2

1 ENSG00000177469 PTRF

1 ENSG00000177707 PVRL3

1 ENSG00000177732 SOX12

1 ENSG00000178031 ADAMTSL1

1 ENSG00000178222 RNF212

1 ENSG00000178947 LINC00086

1 ENSG00000179104 TMTC2

1 ENSG00000179348 GATA2

1 ENSG00000179431 FJX1

1 ENSG00000179776 CDH5

1 ENSG00000180739 S1PR5

1 ENSG00000180875 GREM2

1 ENSG00000181104 F2R

1 ENSG00000182175 RGMA

1 ENSG00000182272 B4GALNT4

1 ENSG00000182492 BGN

1 ENSG00000182534 MXRA7

1 ENSG00000182621 PLCB1

1 ENSG00000182871 COL18A1

1 ENSG00000182985 CADM1

1 ENSG00000183087 GAS6

1 ENSG00000183160 TMEM119

1 ENSG00000183722 LHFP

1 ENSG00000183729 NPBWR1

1 ENSG00000183734 ASCL2

1 ENSG00000183853 KIRREL

1 ENSG00000183963 SMTN

1 ENSG00000184113 CLDN5

1 ENSG00000184564 SLITRK6

1 ENSG00000184916 JAG2

1 ENSG00000184985 SORCS2

1 ENSG00000185070 FLRT2

1 ENSG00000185418 TARSL2

1 ENSG00000185652 NTF3

1 ENSG00000185668 POU3F1

1 ENSG00000185924 RTN4RL1

1 ENSG00000186260 MKL2

1 ENSG00000186318 BACE1

1 ENSG00000186462 NAP1L2

1 ENSG00000186732 MPPED1

1 ENSG00000186994 KANK3

1 ENSG00000186998 EMID1

1 ENSG00000187068 C3orf70

1 ENSG00000187134 AKR1C1

1 ENSG00000187193 MT1X

1 ENSG00000187244 BCAM

1 ENSG00000187513 GJA4

1 ENSG00000187678 SPRY4

1 ENSG00000187720 THSD4

1 ENSG00000187955 COL14A1

1 ENSG00000188153 COL4A5

1 ENSG00000188677 PARVB

1 ENSG00000189376 C8orf76

1 ENSG00000196139 AKR1C3

1 ENSG00000196569 MUD2

1 ENSG00000197256 KANK2

1 ENSG00000197321 SVIL

1 ENSG00000197380 DACT3

1 ENSG00000197461 PDGFA

1 ENSG00000197467 COL13A1

1 ENSG00000197496 SLC2A10

1 ENSG00000197565 COL4A6

1 ENSG00000197614 MFAP5

1 ENSG00000197696 NMB

1 ENSG00000198300 PEG3

1 ENSG00000198719 DLL1

1 ENSG00000198728 LDB1

1 ENSG00000198835 GJC2

1 ENSG00000198853 RUSC2

1 ENSG00000198873 GRK5

1 ENSG00000198885 ITPRIPL1

1 ENSG00000204175 GPRIN2

1 ENSG00000204262 COL5A2

1 ENSG00000204301 NOTCH4

1 ENSG00000205795 CYS1

1 ENSG00000211450 C11orf31

1 ENSG00000212747 FAM127C

1 ENSG00000213689 TREX1

1 ENSG00000213903 LTB4R

1 ENSG00000214860 EVPLL

1 ENSG00000215218 UBE2QL1

1 ENSG00000221866 PLXNA4

1 ENSG00000221968 FADS3

1 ENSG00000224652 LINC00885

1 ENSG00000225950 NTF4

1 ENSG00000229852

1 ENSG00000230937 MIR205HG

1 ENSG00000231789

1 ENSG00000239911 PRKAG2-AS1

1 ENSG00000240583 AQP1

1 ENSG00000240771 ARHGEF25

1 ENSG00000241127 YAE1D1

1 ENSG00000241644 INMT

1 ENSG00000243244 STON1

1 ENSG00000250685

1 ENSG00000251322 SHANK3

1 ENSG00000256309

1 ENSG00000257026

1 ENSG00000269113 TRABD2B

1 ENSG00000269190 FBXO17

1 ENSG00000269905

1 ENSG00000272327

1 ENSG00000272734 ADIRF-AS1

2 ENSG00000001631 KRIT1

2 ENSG00000002016 RAD52

2 ENSG00000003756 RBM5

2 ENSG00000004534 RBM6

2 ENSG00000004777 ARHGAP33

2 ENSG00000006025 OSBPL7

2 ENSG00000006194 ZNF263

2 ENSG00000006530 AGK

2 ENSG00000007392 LUC7L

2 ENSG00000008128 CDK11A

2 ENSG00000009724 MASP2

2 ENSG00000011021 CLCN6

2 ENSG00000011243 AKAP8L

2 ENSG00000011376 LARS2

2 ENSG00000013441 CLK1

2 ENSG00000013561 RNF14

2 ENSG00000018189 RUFY3

2 ENSG00000028310 BRD9

2 ENSG00000032219 ARID4A

2 ENSG00000033030 ZCCHC8

2 ENSG00000038358 EDC4

2 ENSG00000044446 PHKA2

2 ENSG00000047634 SCML1

2 ENSG00000051009 FAM160A2

2 ENSG00000053438 NNAT

2 ENSG00000055955 ITIH4

2 ENSG00000056558 TRAF1

2 ENSG00000058673 ZC3H11A

2 ENSG00000059588 TARBP1

2 ENSG00000061936 SFSWAP

2 ENSG00000061987 MON2

2 ENSG00000064607 SUGP2

2 ENSG00000064687 ABCA7

2 ENSG00000067191 CACNB1

2 ENSG00000068697 LAPTM4A

2 ENSG00000068745 IP6K2

2 ENSG00000069493 CLEC2D

2 ENSG00000070476 ZXDC

2 ENSG00000070610 GBA2

2 ENSG00000070669 ASNS

2 ENSG00000073605 GSDMB

2 ENSG00000074582 BCS1L

2 ENSG00000074696 PTPLAD1

2 ENSG00000075413 MARK3

2 ENSG00000075826 SEC31B

2 ENSG00000077458 FAM76B

2 ENSG00000078403 MLLT10

2 ENSG00000079134 THOC1

2 ENSG00000081019 RSBN1

2 ENSG00000081665 ZNF506

2 ENSG00000081791 KIAA0141

2 ENSG00000082258 CCNT2

2 ENSG00000084463 WBP11

2 ENSG00000085465 OVGP1

2 ENSG00000087087 SRRT

2 ENSG00000087157 PGS1

2 ENSG00000088038 CNOT3

2 ENSG00000088448 ANKRD10

2 ENSG00000089280 FUS

2 ENSG00000090432 MUL1

2 ENSG00000090905 TNRC6A

2 ENSG00000092094 OSGEP

2 ENSG00000092529 CAPN3

2 ENSG00000094631 HDAC6

2 ENSG00000094914 AAAS

2 ENSG00000095066 HOOK2

2 ENSG00000095564 BTAF1

2 ENSG00000099251 HSD17B7P2

2 ENSG00000099940 SNAP29

2 ENSG00000099949 LZTR1

2 ENSG00000100038 TOP3B

2 ENSG00000100068 LRP5L

2 ENSG00000100197 CYP2D6

2 ENSG00000100201 DDX17

2 ENSG00000100288 CHKB

2 ENSG00000100416 TRMU

2 ENSG00000100445 SDR39U1

2 ENSG00000100483 VCPKMT

2 ENSG00000100650 SRSF5

2 ENSG00000100726 TELO2

2 ENSG00000100813 ACIN1

2 ENSG00000100836 PABPN1

2 ENSG00000100941 PNN

2 ENSG00000101049 SGK2

2 ENSG00000101104 PABPC1L

2 ENSG00000101901 ALG13

2 ENSG00000102057 KCND1

2 ENSG00000102125 TAZ

2 ENSG00000102287 GABRE

2 ENSG00000102878 HSF4

2 ENSG00000102901 CENPT

2 ENSG00000102908 NFAT5

2 ENSG00000103091 WDR59

2 ENSG00000103168 TAF1C

2 ENSG00000104365 IKBKB

2 ENSG00000104852 SNRNP70

2 ENSG00000104957 CCDC130

2 ENSG00000105127 AKAP8

2 ENSG00000105136 ZNF419

2 ENSG00000105612 DNASE2

2 ENSG00000105875 WDR91

2 ENSG00000106133 NSUN5P2

2 ENSG00000106344 RBM28

2 ENSG00000106608 URGCP

2 ENSG00000106635 BCL7B

2 ENSG00000108100 CCNY

2 ENSG00000108296 CWC25

2 ENSG00000108389 MTMR4

2 ENSG00000108465 CDK5RAP3

2 ENSG00000108474 PIGL

2 ENSG00000108654 DDX5

2 ENSG00000108773 KAT2A

2 ENSG00000108799 EZH1

2 ENSG00000108848 LUC7L3

2 ENSG00000108963 DPH1

2 ENSG00000109046 WSB1

2 ENSG00000109063 MYH3

2 ENSG00000109920 FNBP4

2 ENSG00000110066 SUV420H1

2 ENSG00000110455 ACCS

2 ENSG00000110721 CHKA

2 ENSG00000110888 CAPRIN2

2 ENSG00000111011 RSRC2

2 ENSG00000111203 ITFG2

2 ENSG00000111231 GPN3

2 ENSG00000111271 ACAD10

2 ENSG00000111364 DDX55

2 ENSG00000111664 GNB3

2 ENSG00000111785 RIC8B

2 ENSG00000111788

2 ENSG00000112309 B3GAT2

2 ENSG00000112357 PEX7

2 ENSG00000112983 BRD8

2 ENSG00000113108 APBB3

2 ENSG00000113240 CLK4

2 ENSG00000113649 TECRG1

2 ENSG00000113971 NPHP3

2 ENSG00000114742 WDR48

2 ENSG00000114770 ABCC5

2 ENSG00000114857 NKTR

2 ENSG00000114982 KANSL3

2 ENSG00000115234 SNX17

2 ENSG00000115282 TTC31

2 ENSG00000115459 ELMOD3

2 ENSG00000115524 SF3B1

2 ENSG00000115875 SRSF7

2 ENSG00000116001 TIA1

2 ENSG00000116350 SRSF4

2 ENSG00000116497 S100PBP

2 ENSG00000116560 SFPQ

2 ENSG00000116580 GON4L

2 ENSG00000116584 ARHGEF2

2 ENSG00000116754 SRSF11

2 ENSG00000116883

2 ENSG00000117360 PRPF3

2 ENSG00000117569 PTBP2

2 ENSG00000117616 C1orf63

2 ENSG00000117862 TXNDC12

2 ENSG00000118482 PHF3

2 ENSG00000118557 PMFBP1

2 ENSG00000119707 RBM25

2 ENSG00000119906 FAM178A

2 ENSG00000120049 KCNIP2

2 ENSG00000120458 MSANTD2

2 ENSG00000120662 MTRF1

2 ENSG00000120798 NR2C1

2 ENSG00000120832 MTERFD3

2 ENSG00000121274 PAPD5

2 ENSG00000121310 ECHDC2

2 ENSG00000121454 LHX4

2 ENSG00000121716 PILRB

2 ENSG00000122085 MTERFD2

2 ENSG00000122257 RBBP6

2 ENSG00000122678 POLM

2 ENSG00000122965 RBM19

2 ENSG00000124098 FAM210B

2 ENSG00000124160 NCOA5

2 ENSG00000124193 SRSF6

2 ENSG00000124222 STX16

2 ENSG00000124593 PRICKLE4

2 ENSG00000124743 KLHL31

2 ENSG00000125447 GGA3

2 ENSG00000125633 CCDC93

2 ENSG00000125814 NAPB

2 ENSG00000125818 PSMF1

2 ENSG00000125846 ZNF133

2 ENSG00000126070 AUG3

2 ENSG00000126217 MCF2L

2 ENSG00000126453 BCL2L12

2 ENSG00000126456 IRF3

2 ENSG00000126500 FLRT1

2 ENSG00000126746 ZNF384

2 ENSG00000126775 ATG14

2 ENSG00000127366 TAS2R5

2 ENSG00000127586 CHTF18

2 ENSG00000127957 PMS2P3

2 ENSG00000128000 ZNF780B

2 ENSG00000128159 TUBGCP6

2 ENSG00000128563 PRKRIP1

2 ENSG00000128699 ORMDL1

2 ENSG00000128915 NARG2

2 ENSG00000129055 ANAPC13

2 ENSG00000129351 ILF3

2 ENSG00000129472 RAB2B

2 ENSG00000129484 PARP2

2 ENSG00000129933 MAU2

2 ENSG00000130254 SAFB2

2 ENSG00000130653 PNPLA7

2 ENSG00000130684 ZNF337

2 ENSG00000130948 HSD17B3

2 ENSG00000131051 RBM39

2 ENSG00000131127 ZNF141

2 ENSG00000131398 KCNC3

2 ENSG00000131591 C1orf159

2 ENSG00000131797 CLUHP3

2 ENSG00000132424 PNISR

2 ENSG00000132485 ZRANB2

2 ENSG00000132680 KIAA0907

2 ENSG00000132780 NASP

2 ENSG00000132793 LFIN3

2 ENSG00000132952 USPL1

2 ENSG00000133318 RTN3

2 ENSG00000133466 C1QTNF6

2 ENSG00000133619 KRBA1

2 ENSG00000133624 ZNF767

2 ENSG00000133858 ZFC3H1

2 ENSG00000134186 PRPF38B

2 ENSG00000134253 TRIM45

2 ENSG00000134453 RBM17

2 ENSG00000134744 ZCCHC11

2 ENSG00000134884 ARGLU1

2 ENSG00000135164 DMTF1

2 ENSG00000135407 AVIL

2 ENSG00000135437 RDH5

2 ENSG00000135473 PAN2

2 ENSG00000135637 CCDC142

2 ENSG00000135740 SLC9A5

2 ENSG00000135976 ANKRD36

2 ENSG00000136271 DDX56

2 ENSG00000136819 C9orf78

2 ENSG00000137185 ZSCAN9

2 ENSG00000137343 ATAT1

2 ENSG00000137504 CREBZF

2 ENSG00000137776 SLTM

2 ENSG00000137802 MAPKBP1

2 ENSG00000137817 PARP6

2 ENSG00000137822 TUBGCP4

2 ENSG00000138050 THUMPD2

2 ENSG00000138109 CYP2C9

2 ENSG00000138658 C4orf21

2 ENSG00000138834 MAPK8IP3

2 ENSG00000139190 VAMP1

2 ENSG00000139574 NPFF

2 ENSG00000139631 CSAD

2 ENSG00000139746 RBM26

2 ENSG00000139908 TSSK4

2 ENSG00000140009 ESR2

2 ENSG00000140181 HERC2P2

2 ENSG00000140398 NEIL1

2 ENSG00000140400 MAN2C1

2 ENSG00000140474 ULK3

2 ENSG00000140488 CELF6

2 ENSG00000140983 RHOT2

2 ENSG00000141068 KSR1

2 ENSG00000141258 SGSM2

2 ENSG00000141551 CSNK1D

2 ENSG00000141564 RPTOR

2 ENSG00000142102 ATHL1

2 ENSG00000142166 IFNAR1

2 ENSG00000142233 NTN5

2 ENSG00000143178 TBX19

2 ENSG00000143183 TMCO1

2 ENSG00000143190 POU2F1

2 ENSG00000143379 SETDB1

2 ENSG00000143434 SEMA6C

2 ENSG00000143442 POGZ

2 ENSG00000143630 HCN3

2 ENSG00000144026 ZNF514

2 ENSG00000144161 ZC3H8

2 ENSG00000144524 COPS7B

2 ENSG00000145020 AMT

2 ENSG00000145029 NICN1

2 ENSG00000145908 ZNF300

2 ENSG00000146021 KLHL3

2 ENSG00000146067 FAM193B

2 ENSG00000146215 CRIP3

2 ENSG00000146556 WASH2P

2 ENSG00000146826 C7orf43

2 ENSG00000146830 GIGYF1

2 ENSG00000146963 C7orf55-LUC7L2

2 ENSG00000147118 ZNF182

2 ENSG00000147121 KRBOX4

2 ENSG00000147162 OGT

2 ENSG00000147174 ACRC

2 ENSG00000147180 ZNF711

2 ENSG00000147437 GNRH1

2 ENSG00000147576 ADHFE1

2 ENSG00000147789 ZNF7

2 ENSG00000147854 UHRF2

2 ENSG00000148200 NR6A1

2 ENSG00000148399 DPH7

2 ENSG00000149532 CPSF7

2 ENSG00000151006 PRSS53

2 ENSG00000151303 AGAP11

2 ENSG00000151376 ME3

2 ENSG00000151849 CENPJ

2 ENSG00000152042 NBPF11

2 ENSG00000152117

2 ENSG00000152433 ZNF547

2 ENSG00000152520 PAN3

2 ENSG00000152527 PLEKHH2

2 ENSG00000152795 HNRNPDL

2 ENSG00000152926 ZNF117

2 ENSG00000153291 SLC25A27

2 ENSG00000153666 GOLGA8I

2 ENSG00000153914 SREK1

2 ENSG00000154144 TBRG1

2 ENSG00000154263 ABCA10

2 ENSG00000154832 CXXC1

2 ENSG00000155229 MMS19

2 ENSG00000155256 ZFYVE27

2 ENSG00000155657 TTN

2 ENSG00000155903 RASA2

2 ENSG00000156639 ZFAND3

2 ENSG00000156642 NPTN

2 ENSG00000157306

2 ENSG00000157741 UBN2

2 ENSG00000157764 BRAF

2 ENSG00000158286 RNF207

2 ENSG00000158805 ZNF276

2 ENSG00000158815 FGF17

2 ENSG00000159086 PAXBP1

2 ENSG00000159140 SON

2 ENSG00000159346 ADIPOR1

2 ENSG00000159461 AMFR

2 ENSG00000160072 ATAD3B

2 ENSG00000160323 ADAMTS13

2 ENSG00000160781 PAQR6

2 ENSG00000160828 STAG3L2

2 ENSG00000160953 MUM1

2 ENSG00000160961 ZNF333

2 ENSG00000161265 U2AF1L4

2 ENSG00000161547 SRSF2

2 ENSG00000161664 ASB16

2 ENSG00000161912 ADCY10P1

2 ENSG00000162086 ZNF75A

2 ENSG00000162231 NXF1

2 ENSG00000162408 NOL9

2 ENSG00000162461 SLC25A34

2 ENSG00000162526 TSSK3

2 ENSG00000162572 SCNN1D

2 ENSG00000162601 MYSM1

2 ENSG00000162650 ATXN7L2

2 ENSG00000162735 PEX19

2 ENSG00000162997 PRORSD1P

2 ENSG00000163354 DCST2

2 ENSG00000163660 CCNL1

2 ENSG00000163714 U2SURP

2 ENSG00000163728 TTC14

2 ENSG00000163867 ZMYM6

2 ENSG00000163945 UVSSA

2 ENSG00000164048 ZNF589

2 ENSG00000164073 MFSD8

2 ENSG00000164074 C4orf29

2 ENSG00000164241 C5orf63

2 ENSG00000164406 LEAP2

2 ENSG00000164548 TRA2A

2 ENSG00000164877 MICALL2

2 ENSG00000164879 CA3

2 ENSG00000165275 TRMT10B

2 ENSG00000165494 PCF11

2 ENSG00000165699 TSC1

2 ENSG00000165792 METTL17

2 ENSG00000165819 METTL3

2 ENSG00000166012 TAF1D

2 ENSG00000166169 POLL

2 ENSG00000166261 ZNF202

2 ENSG00000166321 NUDT13

2 ENSG00000166343 MSS51

2 ENSG00000166405 RIC3

2 ENSG00000166432 ZMAT1

2 ENSG00000166436 TRIM66

2 ENSG00000166667 SPDYE6

2 ENSG00000166762 CATSPER2

2 ENSG00000166801 FAM111A

2 ENSG00000166887 VPS39

2 ENSG00000167280 ENGASE

2 ENSG00000167302 ENTHD2

2 ENSG00000167371 PRRT2

2 ENSG00000167380 ZNF226

2 ENSG00000167524

2 ENSG00000167549 CORO6

2 ENSG00000167566 NCKAP5L

2 ENSG00000167615 LENG8

2 ENSG00000167674

2 ENSG00000167702 KIFC2

2 ENSG00000167766 ZNF83

2 ENSG00000167978 SRRM2

2 ENSG00000168005 C11orf84

2 ENSG00000168010 ATG16L2

2 ENSG00000168066 SF1

2 ENSG00000168096 ANKS3

2 ENSG00000168137 SETD5

2 ENSG00000168310 IRF2

2 ENSG00000168395 ENG5

2 ENSG00000168566 SNRNP48

2 ENSG00000168614 NBPF9

2 ENSG00000168876 ANKRD49

2 ENSG00000168887 C2orf68

2 ENSG00000168939 SPRY3

2 ENSG00000168970 JMJD7-PLA2G4B

2 ENSG00000169045 HNRNPH1

2 ENSG00000169131 ZNF354A

2 ENSG00000169203

2 ENSG00000169246 NPIPB3

2 ENSG00000169592 INO80E

2 ENSG00000169660 HEXDC

2 ENSG00000169885 CALML6

2 ENSG00000169914 OTUD3

2 ENSG00000170049 KCNAB3

2 ENSG00000170074 FAM153A

2 ENSG00000170234 PWWP2A

2 ENSG00000170581 STAT2

2 ENSG00000170919 TPT1-AS1

2 ENSG00000170949 ZNF160

2 ENSG00000171163 ZNF692

2 ENSG00000171456 ASXL1

2 ENSG00000171824 EXOSC10

2 ENSG00000172273 HINFP

2 ENSG00000172345 STARD5

2 ENSG00000172354 GNB2

2 ENSG00000172650 AGAP5

2 ENSG00000172732 MUS81

2 ENSG00000172803 SNX32

2 ENSG00000172890 NADSYN1

2 ENSG00000173064 HECTD4

2 ENSG00000173209 AHSA2

2 ENSG00000173275 ZNF449

2 ENSG00000173531 MST1

2 ENSG00000173575 CHD2

2 ENSG00000173681 CXorf23

2 ENSG00000173991 TCAP

2 ENSG00000174093

2 ENSG00000174194 AGAP8

2 ENSG00000174353 STAG3L3

2 ENSG00000174652 ZNF266

2 ENSG00000175066 GK5

2 ENSG00000175265 GOLGA8A

2 ENSG00000175309 PHYKPL

2 ENSG00000175322 ZNF519

2 ENSG00000175455 CCDC14

2 ENSG00000175787 ZNF169

2 ENSG00000176444 CLK2

2 ENSG00000176681 LRRC37A

2 ENSG00000176946 THAP4

2 ENSG00000177042 TMEM80

2 ENSG00000177202 SPACA4

2 ENSG00000177225 PDDC1

2 ENSG00000177479 ARIH2

2 ENSG00000177485 ZBTB33

2 ENSG00000177595 PIDD

2 ENSG00000177853 ZNF518A

2 ENSG00000177943 MAMDC4

2 ENSG00000178028 DMAP1

2 ENSG00000178038 ALS2CL

2 ENSG00000178188 SH2B1

2 ENSG00000178252 WDR6

2 ENSG00000178338 ZNF354B

2 ENSG00000178397 FAM220A

2 ENSG00000178567 EPM2AIP1

2 ENSG00000178761 FAM219B

2 ENSG00000179304 FAM156B

2 ENSG00000179406 LINC00174

2 ENSG00000179979 CRIPAK

2 ENSG00000180113 TDRD6

2 ENSG00000180855 ZNF443

2 ENSG00000180902 D2HGDH

2 ENSG00000181045 SLC26A11

2 ENSG00000181523 SGSH

2 ENSG00000181852 RNF41

2 ENSG00000182230 FAM153B

2 ENSG00000182308 DCAF4L1

2 ENSG00000182310 SPACA6P

2 ENSG00000182324 KCNJ14

2 ENSG00000182378 PLCXD1

2 ENSG00000182473 EXOC7

2 ENSG00000182484 WASH6P

2 ENSG00000182646 FAM156A

2 ENSG00000182685 BRICD5

2 ENSG00000182796 TMEM198B

2 ENSG00000182841 RRP7B

2 ENSG00000182873

2 ENSG00000182944 EWSR1

2 ENSG00000182983 ZNF662

2 ENSG00000182986 ZNF320

2 ENSG00000183281 PLGLB1

2 ENSG00000183291

2 ENSG00000183423 LRIT3

2 ENSG00000183718 TRIM52

2 ENSG00000184343 SRPK3

2 ENSG00000184402 SS18L1

2 ENSG00000184441

2 ENSG00000184465 WDR27

2 ENSG00000184634 MED12

2 ENSG00000184640 9-Sep

2 ENSG00000184677 ZBTB40

2 ENSG00000184787 UBE2G2

2 ENSG00000184863 RBM33

2 ENSG00000184925 LCN12

2 ENSG00000185101 YEAR9

2 ENSG00000185122 HSF1

2 ENSG00000185128 TBC1D3F

2 ENSG00000185189 NRBP2

2 ENSG00000185219 ZNF445

2 ENSG00000185246 PRPF39

2 ENSG00000185324 CDK10

2 ENSG00000185485 SDHAP1

2 ENSG00000185596 WASH3P

2 ENSG00000185684 EP400NL

2 ENSG00000185829 ARL17A

2 ENSG00000185842 DNAH14

2 ENSG00000185864 NPIPB4

2 ENSG00000185946 RNPC3

2 ENSG00000185986 SDHAP3

2 ENSG00000186088 GSAP

2 ENSG00000186166 CCDC84

2 ENSG00000186204 CYP4F12

2 ENSG00000186275 NBPF12

2 ENSG00000186283 TOR3A

2 ENSG00000186301 MST1P2

2 ENSG00000186376 ZNF75D

2 ENSG00000186566 GPATCH8

2 ENSG00000186567 CEACAM19

2 ENSG00000186715 MST1L

2 ENSG00000186812 ZNF397

2 ENSG00000186814 ZSCAN30

2 ENSG00000186834 HEXIM1

2 ENSG00000186908 ZDHHC17

2 ENSG00000187066 TMEM262

2 ENSG00000187961 KLHL17

2 ENSG00000188206 HNRNPU-AS1

2 ENSG00000188227 ZNF793

2 ENSG00000188234 AGAP4

2 ENSG00000188428 BLOC1S5

2 ENSG00000188529 SRSF10

2 ENSG00000188554 NBR1

2 ENSG00000188738 FSIP2

2 ENSG00000188811 NHLRC3

2 ENSG00000188827 SLX4

2 ENSG00000189007 ADAT2

2 ENSG00000189136 UBE2Q2P1

2 ENSG00000196074 SYCP2

2 ENSG00000196123 KIAA0895L

2 ENSG00000196295

2 ENSG00000196296 ATP2A1

2 ENSG00000196387 ZNF140

2 ENSG00000196409 ZNF658

2 ENSG00000196440 ARMCX4

2 ENSG00000196644 GPR89C

2 ENSG00000196648 GOLGA6L20

2 ENSG00000196670 ZFP62

2 ENSG00000196689 TRPV1

2 ENSG00000196696 PDXDC2P

2 ENSG00000196757 ZNF700

2 ENSG00000196912 ANKRD36B

2 ENSG00000197119 SLC25A29

2 ENSG00000197124 ZNF682

2 ENSG00000197162 ZNF785

2 ENSG00000197182

2 ENSG00000197343 ZNF655

2 ENSG00000197558 SSPO

2 ENSG00000197608 ZNF841

2 ENSG00000197681 TBC1D3

2 ENSG00000197774 EME2

2 ENSG00000197857 ZNF44

2 ENSG00000197948 FCHSD1

2 ENSG00000197961 ZNF121

2 ENSG00000197976 AKAP17A

2 ENSG00000197989 SNHG12

2 ENSG00000198035 AGAP9

2 ENSG00000198040 ZNF84

2 ENSG00000198064

2 ENSG00000198105 ZNF248

2 ENSG00000198150

2 ENSG00000198198 SZT2

2 ENSG00000198231 DDX42

2 ENSG00000198276 UCKL1

2 ENSG00000198393 ZNF26

2 ENSG00000198556 ZNF789

2 ENSG00000198563 DDX39B

2 ENSG00000198590 C3orf35

2 ENSG00000198625 MDM4

2 ENSG00000198799 LRIG2

2 ENSG00000203392

2 ENSG00000203667 COX20

2 ENSG00000203709 C1orf132

2 ENSG00000203761 MSTO2P

2 ENSG00000203815 FAM231D

2 ENSG00000203880 PCMTD2

2 ENSG00000204149 AGAP6

2 ENSG00000204164 BMS1P5

2 ENSG00000204271 SPIN3

2 ENSG00000204305 AGER

2 ENSG00000204311 DFNB59

2 ENSG00000204348 DXO

2 ENSG00000204351 SKIV2L

2 ENSG00000204410 MSH5

2 ENSG00000204514 ZNF814

2 ENSG00000204576 PRR3

2 ENSG00000204681 GABBR1

2 ENSG00000204946 ZNF783

2 ENSG00000205047

2 ENSG00000205085 FAM71F2

2 ENSG00000205238 SPDYE2

2 ENSG00000205307 SAP25

2 ENSG00000205560 CPT1B

2 ENSG00000205583 STAG3L1

2 ENSG00000205885 C1RL-AS1

2 ENSG00000205890

2 ENSG00000205923 CEMP1

2 ENSG00000205959

2 ENSG00000206149 HERC2P9

2 ENSG00000206417 H1FX-AS1

2 ENSG00000206573 SETD5-AS1

2 ENSG00000211454 AKR7L

2 ENSG000002212123 PRR22

2 ENSG00000212127 TAS2R14

2 ENSG00000212694

2 ENSG00000213139 CRYGS

2 ENSG00000213190 MLLT11

2 ENSG00000213246 SUPT4H1

2 ENSG00000213339 QTRT1

2 ENSG00000213347 MXD3

2 ENSG00000213443

2 ENSG00000213599 SLX1A-SULT1A3

2 ENSG00000213901 SLC23A3

2 ENSG00000213918 DNASE1

2 ENSG00000213983 AP1G2

2 ENSG00000213999 MEF2B

2 ENSG00000214021 TTLL3

2 ENSG00000214135

2 ENSG00000214176 PLEKHM1P

2 ENSG00000214279

2 ENSG00000214331

2 ENSG00000214455 RCN1P2

2 ENSG00000214756 METTL12

2 ENSG00000214765 SEPT7P2

2 ENSG00000214783 POLR2J4

2 ENSG00000214826 DDX12P

2 ENSG00000214827 MTCP1

2 ENSG00000215022

2 ENSG00000215041 NEURL4

2 ENSG00000215126 CBWD7

2 ENSG00000215158

2 ENSG00000215252 GOLGA8B

2 ENSG00000215298

2 ENSG00000215375 MYL5

2 ENSG00000215417 MIR17HG

2 ENSG00000215424 MCM3AP-AS1

2 ENSG00000215440 NPEPL1

2 ENSG00000215513 PI4KAP1

2 ENSG00000215769

2 ENSG00000215788 TNFRSF25

2 ENSG00000216937 CCDC7

2 ENSG00000218891 ZNF579

2 ENSG00000220201 ZGLP1

2 ENSG00000221944 TIGD1

2 ENSG00000221978 CCNL2

2 ENSG00000223509

2 ENSG00000223705 NSUN5P1

2 ENSG00000223745

2 ENSG00000223839 FAM95B1

2 ENSG00000223959 AFG3L1P

2 ENSG00000224186 C5orf66

2 ENSG00000224660 SH3BP5-AS1

2 ENSG00000224956

2 ENSG00000224975 INE1

2 ENSG00000225032

2 ENSG00000225138

2 ENSG00000225313

2 ENSG00000225373 WASH5P

2 ENSG00000225697 SLC26A6

2 ENSG00000225828 FAM229A

2 ENSG00000225855 RUSC1-AS1

2 ENSG00000225892

2 ENSG00000226232

2 ENSG00000226332

2 ENSG00000226696 LENG8-AS1

2 ENSG00000226763 SRRM5

2 ENSG00000227232 WASH7P

2 ENSG00000227543 SPAG5-AS1

2 ENSG00000227671 MIR3916

2 ENSG00000227896

2 ENSG00000228274

2 ENSG00000228315 GUSBP11

2 ENSG00000228393 LINC01004

2 ENSG00000228409 CCT6P1

2 ENSG00000228492 RAB11FIP1P1

2 ENSG00000228784 LINC00954

2 ENSG00000229180

2 ENSG00000229186 ADAM1A

2 ENSG00000230124

2 ENSG00000230373 GOLGA6L5P

2 ENSG00000230454

2 ENSG00000230551

2 ENSG00000230606

2 ENSG00000230715

2 ENSG00000232807

2 ENSG00000233137

2 ENSG00000233175

2 ENSG00000233184

2 ENSG00000234072

2 ENSG00000234290

2 ENSG00000234353

2 ENSG00000234420 ZNF37BP

2 ENSG00000234585 CCT6P3

2 ENSG00000234616 JRK

2 ENSG00000234631

2 ENSG00000234769 WASH4P

2 ENSG00000234771

2 ENSG00000234912 LINC00338

2 ENSG00000235016

2 ENSG00000235194 PPP1R3E

2 ENSG00000235381

2 ENSG00000235703 LINC00894

2 ENSG00000235999

2 ENSG00000236017 ASMTL-AS1

2 ENSG00000236088 COX10-AS1

2 ENSG00000236144

2 ENSG00000236255

2 ENSG00000236287 ZBED5

2 ENSG00000236438 FAM157A

2 ENSG00000237298 TTN-AS1

2 ENSG00000237441 RGL2

2 ENSG00000237491

2 ENSG00000238083 LRRC37A2

2 ENSG00000239382 ALKBH6

2 ENSG00000239665

2 ENSG00000240038 AMY2B

2 ENSG00000240053 LY6G5B

2 ENSG00000240288 GHRLOS

2 ENSG00000240291

2 ENSG00000240731

2 ENSG00000241014

2 ENSG00000241058 NSUN6

2 ENSG00000241404 EGFL8

2 ENSG00000241489

2 ENSG00000241528

2 ENSG00000241769 LINC00893

2 ENSG00000242028 HYPK

2 ENSG00000242125 SNHG3

2 ENSG00000242282

2 ENSG00000242384 TBC1D3H

2 ENSG00000242802 AP5Z1

2 ENSG00000242861

2 ENSG00000242866 STRC

2 ENSG00000243155

2 ENSG00000243302

2 ENSG00000243452 NBPF15

2 ENSG00000243679

2 ENSG00000243708 PLA2G4B

2 ENSG00000243716 NPIPB5

2 ENSG00000244119 PDCL3P4

2 ENSG00000244151

2 ENSG00000244480

2 ENSG00000244560

2 ENSG00000244754 N4BP2L2

2 ENSG00000244879 GABPB1-AS1

2 ENSG00000245149 RNF139-AS1

2 ENSG00000245532 NEAT1

2 ENSG00000245849 RAD51-AS1

2 ENSG00000245970

2 ENSG00000246090

2 ENSG00000246339 EXTL3-AS1

2 ENSG00000246451

2 ENSG00000246922 UBAP1L

2 ENSG00000247679

2 ENSG00000248019 FAM13A-AS1

2 ENSG00000248124 RRN3P1

2 ENSG00000249087 C1orf213

2 ENSG00000250067 YJEFN3

2 ENSG00000250506 CDK3

2 ENSG00000251022 THAP9-AS1

2 ENSG00000251136

2 ENSG00000251247 ZNF345

2 ENSG00000251364

2 ENSG00000251369 ZNF550

2 ENSG00000251432

2 ENSG00000251562 MALAT1

2 ENSG00000252690 SCARNA15

2 ENSG00000253106

2 ENSG00000253200

2 ENSG00000253352 TUG1

2 ENSG00000254363

2 ENSG00000254413 CHKB-CPT1B

2 ENSG00000254815

2 ENSG00000254995 STX16-NPEPL1

2 ENSG00000255031

2 ENSG00000255182

2 ENSG00000255717 SNHG1

2 ENSG00000256028

2 ENSG00000256223 ZNF10

2 ENSG00000256294 ZNF225

2 ENSG00000256525 POLG2

2 ENSG00000256667 KLRAP1

2 ENSG00000257511

2 ENSG00000257621

2 ENSG00000258297

2 ENSG00000258311

2 ENSG00000258441 LINC00641

2 ENSG00000258461

2 ENSG00000258472

2 ENSG00000258634

2 ENSG00000258727

2 ENSG00000258839 MC1R

2 ENSG00000258890 CEP95

2 ENSG00000259820

2 ENSG00000259865

2 ENSG00000259891

2 ENSG00000259972

2 ENSG00000259994

2 ENSG00000260091

2 ENSG00000260236

2 ENSG00000260257

2 ENSG00000260296

2 ENSG00000260306

2 ENSG00000260565 ERVK13-1

2 ENSG00000260669

2 ENSG00000260711

2 ENSG00000260729

2 ENSG00000260772

2 ENSG00000260778 MIR940

2 ENSG00000260837

2 ENSG00000260872

2 ENSG00000260917

2 ENSG00000260924

2 ENSG00000260942 CAPN10-AS1

2 ENSG00000261015

2 ENSG00000261052 SULT1A3

2 ENSG00000261067

2 ENSG00000261087

2 ENSG00000261136

2 ENSG00000261139

2 ENSG00000261254

2 ENSG00000261286

2 ENSG00000261324

2 ENSG00000261326

2 ENSG00000261355

2 ENSG00000261408 TEN1-CDK3

2 ENSG00000261460

2 ENSG00000261488

2 ENSG00000261490

2 ENSG00000261505

2 ENSG00000261526

2 ENSG00000261556

2 ENSG00000261584

2 ENSG00000261613

2 ENSG00000261799

2 ENSG00000262580

2 ENSG00000262877

2 ENSG00000263020

2 ENSG00000263126

2 ENSG00000263198

2 ENSG00000263272

2 ENSG00000263276

2 ENSG00000263327 TAPT1-AS1

2 ENSG00000264098

2 ENSG00000264112

2 ENSG00000264538

2 ENSG00000264772 SNORA67

2 ENSG00000265298

2 ENSG00000265629

2 ENSG00000265690

2 ENSG00000266086

2 ENSG00000266714 MYO15B

2 ENSG00000267152

2 ENSG00000267244

2 ENSG00000267281

2 ENSG00000267283

2 ENSG00000267680 ZNF224

2 ENSG00000267896

2 ENSG00000267940

2 ENSG00000268030

2 ENSG00000268220

2 ENSG00000268471 MIR4453

2 ENSG00000269131

2 ENSG00000269352

2 ENSG00000269399

2 ENSG00000269680

2 ENSG00000269751

2 ENSG00000269821 KCNQ1OT1

2 ENSG00000269928

2 ENSG00000269929

2 ENSG00000269958

2 ENSG00000270012

2 ENSG00000270015

2 ENSG00000270055

2 ENSG00000270069

2 ENSG00000270189

2 ENSG00000270574

2 ENSG00000271344

2 ENSG00000271430

2 ENSG00000271529 CICP14

2 ENSG00000271533

2 ENSG00000271795

2 ENSG00000271816

2 ENSG00000271857

2 ENSG00000271870

2 ENSG00000271895

2 ENSG00000271975

2 ENSG00000271997

2 ENSG00000272077

2 ENSG00000272141

2 ENSG00000272145 NFYC-AS1

2 ENSG00000272216

2 ENSG00000272316

2 ENSG00000272356

2 ENSG00000272455

2 ENSG00000272505 2 ENSG00000272578 2 ENSG00000272589 ZSWIM8-AS1 2 ENSG00000272631 2 ENSG00000272645 2 ENSG00000272658 2 ENSG00000272668 2 ENSG00000272720 STAG3L5P-PVRIG2P-2 ENSG00000272752

PILRB 2 ENSG00000272782 2 ENSG00000272782 2 ENSG00000272849 2 ENSG00000272916 2 ENSG00000272977 2 ENSG00000273000 2 ENSG00000273131 2 ENSG00000273137 2 ENSG00000273151 2 ENSG00000273271 2 ENSG00000273373 2 ENSG00000273466708 ENSG0000000034

3 ENSG00000108551 RASD1

3 ENSG00000120129 DUSP1

3 ENSG00000120738 EGR1

3 ENSG00000123358 NR4A1

3 ENSG00000125740 FOSB

3 ENSG00000128016 ZFP36

3 ENSG00000128342 LIF

3 ENSG00000137331 IER3

3 ENSG00000139318 DUSP6

3 ENSG00000142178 SIK1

3 ENSG00000148339 SLC25A25

3 ENSG00000153234 NR4A2

3 ENSG00000158050 DUSP2

3 ENSG00000159388 BTG2

3 ENSG00000160888 IER2

3 ENSG00000170345 FOS

3 ENSG00000171223 JUNB

3 ENSG00000177606 JUN

3 ENSG00000198355 PIM3

4 ENSG00000062582 MRPS24

4 ENSG00000065518 NDUFB4

4 ENSG00000090266 NDUFB2

4 ENSG00000099341 PSMD8

4 ENSG00000099795 NDUFB7

4 ENSG00000100216 TOMM22

4 ENSG00000103363 TCEB2

4 ENSG00000106153 CHCHD2

4 ENSG00000110801 PSMD9

4 ENSG00000111639 MRPL51

4 ENSG00000111775 COX6A1

4 ENSG00000112695 COX7A2

4 ENSG00000116459 ATP5F1

4 ENSG00000119013 NDUFB3

4 ENSG00000120509 PDZD11

4 ENSG00000125356 NDUFA1

4 ENSG00000125445 MRPS7

4 ENSG00000125995 ROMO1

4 ENSG00000126267 COX6B1

4 ENSG00000126768 TIMM17B

4 ENSG00000127540 UQCR11

4 ENSG00000127774 EMC6

4 ENSG00000131174 COX7B

4 ENSG00000135441 BLOC1S1

4 ENSG00000135940 COX5B

4 ENSG00000136930 PSMB7

4 ENSG00000140990 NDUFB10

4 ENSG00000141552 ANAPC11

4 ENSG00000141759 TXNL4A

4 ENSG00000143977 SNRPG

4 ENSG00000145494 NDUFS6

4 ENSG00000150779 TIMM8B

4 ENSG00000151366 NDUFC2

4 ENSG00000155368 DBI

4 ENSG00000156411 C14orf2

4 ENSG00000163634 THOC7

4 ENSG00000164405 UQCRQ

4 ENSG00000164919 COX6C

4 ENSG00000165264 NDUFB6

4 ENSG00000165283 STOML2

4 ENSG00000166136 NDUFB8

4 ENSG00000169020 ATP5I

4 ENSG00000169021 UQCRFS1

4 ENSG00000171421 MRPL36

4 ENSG00000172428 MYEOV2

4 ENSG00000172586 CHCHD1

4 ENSG00000173436 MINOS1

4 ENSG00000173915 USMG5

4 ENSG00000176340 COX8A

4 ENSG00000177700 POLR2L

4 ENSG00000178307 TMEM11

4 ENSG00000178741 COX5A

4 ENSG00000183617 MRPL54

4 ENSG00000184076 UQCR10

4 ENSG00000184752 NDUFA12

4 ENSG00000185721 DRG1

4 ENSG00000186010 NDUFA13

4 ENSG00000188612 SUMO2

4 ENSG00000189043 NDUFA4

4 ENSG00000198522 GPN1

4 ENSG00000204922 C11orf83

4 ENSG00000213619 NDUFS3

4 ENSG00000241468 ATP5J2

4 ENSG00000262814 MRPL12

5 ENSG00000000460 C1orf112

5 ENSG00000004142 POLDIP2

5 ENSG00000006634 DBF4

5 ENSG00000007968 E2F2

5 ENSG00000010292 NCAPD2

5 ENSG00000011426 ANLN

5 ENSG00000024526 DEPDC1

5 ENSG00000034063 UHRF1

5 ENSG00000040275 SPDL1

5 ENSG00000048140 TSPAN17

5 ENSG00000049541 RFC2

5 ENSG00000051180 RAD51

5 ENSG00000055044 NOP58

5 ENSG00000066279 ASPM

5 ENSG00000068489 PRR11

5 ENSG00000072571 HMMR

5 ENSG00000075218 GTSE1

5 ENSG00000075702 WDR62

5 ENSG00000077152 UBE2T

5 ENSG00000080986 NDC80

5 ENSG00000085840 ORC1

5 ENSG00000085999 RAD54L

5 ENSG00000087111 PIGS

5 ENSG00000087586 AURKA

5 ENSG00000088325 TPX2

5 ENSG00000089685 BIRC5

5 ENSG000000090889 KIF4A

5 ENSG00000091651 ORC6

5 ENSG00000093009 CDC45

5 ENSG00000094804 CDC6

5 ENSG00000097046 CDC7

5 ENSG00000100297 MCM5

5 ENSG00000100526 CDKN3

5 ENSG00000100600 LGMN

5 ENSG00000101003 GINS1

5 ENSG00000101057 MYBL2

5 ENSG00000101412 E2F1

5 ENSG00000101945 SUV39H1

5 ENSG00000102384 CENPI

5 ENSG00000104064 GABPB1

5 ENSG00000104738 MCM4

5 ENSG00000104889 RNASEH2A

5 ENSG00000105011 ASF1B

5 ENSG00000105135 ILVBL

5 ENSG00000106462 EZH2

5 ENSG00000108106 UBE2S

5 ENSG00000109805 NCAPG

5 ENSG00000111206 FOXM1

5 ENSG00000111247 RAD51AP1

5 ENSG00000111445 RFC5

5 ENSG00000111602 TIMELESS

5 ENSG00000112118 MCM3

5 ENSG00000112578 BYSL

5 ENSG00000112742 TTK

5 ENSG00000112984 KIF20A

5 ENSG00000113368 LMNB1

5 ENSG00000113810 SMC4

5 ENSG00000116212 LRRC42

5 ENSG00000116478 HDAC1

5 ENSG00000116830 TTF2

5 ENSG00000117399 CDC20

5 ENSG00000117632 STMN1

5 ENSG00000117724 CENPF

5 ENSG00000118193 KIF14

5 ENSG00000119969 HELLS

5 ENSG00000120254 MTHFD1L

5 ENSG00000120539 MASTL

5 ENSG00000120647 CCDC77

5 ENSG00000120802 TMPO

5 ENSG00000121152 NCAPH

5 ENSG00000121621 KIF18A

5 ENSG00000122483 CCDC18

5 ENSG00000122566 HNRNPA2B1

5 ENSG00000122952 ZWINT

5 ENSG00000123219 CENPK

5 ENSG00000123416 TUBA1B

5 ENSG00000123485 HJURP

5 ENSG00000123975 CKS2

5 ENSG00000124207 CSE1L

5 ENSG00000124766 SOX4

5 ENSG00000125319 C17orf53

5 ENSG00000125944 HNRNPR

5 ENSG00000126787 DLGAP5

5 ENSG00000127564 PKMYT1

5 ENSG00000128274 A4GALT

5 ENSG00000128944 KNSTRIN

5 ENSG00000129195 FAM64A

5 ENSG00000130202 PVRL2

5 ENSG00000131153 GINS2

5 ENSG00000131269 ABCB7

5 ENSG00000131747 TOP2A

5 ENSG00000132313 MRPL35

5 ENSG00000132646 PCNA

5 ENSG00000134057 CCNB1

5 ENSG00000134690 CDCA8

5 ENSG00000135451 TROAP

5 ENSG00000135476 ESPL1

5 ENSG00000135763 URB2

5 ENSG00000135823 STX6

5 ENSG00000136108 CKAP2

5 ENSG00000136122 BORA

5 ENSG00000136492 BRIP1

5 ENSG00000136943 CTSV

5 ENSG00000137449 CPEB2

5 ENSG00000137804 NUSAP1

5 ENSG00000137807 KIF23

5 ENSG00000137812 CASC5

5 ENSG00000138092 CENPO

5 ENSG00000138160 KIF11

5 ENSG00000138180 CEP55

5 ENSG00000138442 WDR12

5 ENSG00000138778 CENPE

5 ENSG00000139618 BRCA2

5 ENSG00000139726 DENR

5 ENSG00000139734 DIAPH3

5 ENSG00000140525 FANCI

5 ENSG00000142731 PLK4

5 ENSG00000142945 KIF2C

5 ENSG00000143228 NUF2

5 ENSG00000143476 DTL

5 ENSG00000143493 INTS7

5 ENSG00000143621 ILF2

5 ENSG00000143942 CHAC2

5 ENSG00000144554 FANCD2

5 ENSG00000145386 CCNA2

5 ENSG00000145604 SKP2

5 ENSG00000145907 G3BP1

5 ENSG00000146410 MTFR2

5 ENSG00000146670 CDCA5

5 ENSG00000146918 NCAPG2

5 ENSG00000147140 NINTH

5 ENSG00000147274 RBMX

5 ENSG00000147536 GINS4

5 ENSG00000148773 MKI67

5 ENSG00000149554 CHEK1

5 ENSG00000151287 TEX30

5 ENSG00000153044 CENPH

5 ENSG00000154839 SKA1

5 ENSG00000154920 EME1

5 ENSG00000156970 BUB1B

5 ENSG00000157456 CCNB2

5 ENSG00000159259 CHAF1B

5 ENSG00000161800 RACGAP1

5 ENSG00000161888 SPC24

5 ENSG00000162062 C16orf59

5 ENSG00000162063 CCNF

5 ENSG00000163507 KIAA1524

5 ENSG00000163808 KIF15

5 ENSG00000163923 RPL39L

5 ENSG00000163950 SLBP

5 ENSG00000164045 CDC25A

5 ENSG00000164109 MAD2L1

5 ENSG00000164611 PTTG1

5 ENSG00000165304 MELK

5 ENSG00000165480 SKA3

5 ENSG00000166451 CENPN

5 ENSG00000166803 KIAA0101

5 ENSG00000166851 PLK1

5 ENSG00000167513 CDT1

5 ENSG00000167900 TK1

5 ENSG00000168078 PBK

5 ENSG00000168393 DTYMK

5 ENSG00000168411 RFWD3

5 ENSG00000168496 FEN1

5 ENSG00000168883 USP39

5 ENSG00000169607 CKAP2L

5 ENSG00000169679 BUB1

5 ENSG00000170312 CDK1

5 ENSG00000171241 SHCBP1

5 ENSG00000171320 ESCO2

5 ENSG00000171848 RRM2

5 ENSG00000173207 CKS1B

5 ENSG00000174442 ZWILCH

5 ENSG00000175063 UBE2C

5 ENSG00000175216 CKAP5

5 ENSG00000175305 CCNE2

5 ENSG00000176890 TYMS

5 ENSG00000177191 B3GNT8

5 ENSG00000178999 AURKB

5 ENSG00000179051 RCC2

5 ENSG00000179115 HUMBUG

5 ENSG00000179632 MAF1

5 ENSG00000182481 KPNA2

5 ENSG00000182628 SKA2

5 ENSG00000183763 TRAIP

5 ENSG00000183814 LIN9

5 ENSG00000183856 IQGAP3

5 ENSG00000184661 CDCA2

5 ENSG00000185480 PARPBP

5 ENSG00000186185 KIF18B

5 ENSG00000186871 ERCC6L

5 ENSG00000187514 PTMA

5 ENSG00000187741 FANCA

5 ENSG00000188486 H2AFX

5 ENSG00000188610 FAM72B

5 ENSG00000189057 FAM111B

5 ENSG00000196419 XRCC6

5 ENSG00000196550 FAM72A

5 ENSG00000196584 XRCC2

5 ENSG00000198331 HYLS1

5 ENSG00000198826 ARHGAP11A

5 ENSG00000198901 PRC1

5 ENSG00000203760 CENPW

5 ENSG00000204392 LSM2

5 ENSG00000213186 TRIM59

5 ENSG00000215784 FAM72D

5 ENSG00000228716 DHFR

5 ENSG00000237649 KIFC1

5 ENSG00000247077 PGAM5

6 ENSG00000001460 STPG1

6 ENSG00000003096 KLHL13

6 ENSG00000003989 SLC7A2

6 ENSG00000004838 ZMYND10

6 ENSG00000004848 ARX

6 ENSG00000005100 DHX33

6 ENSG00000005448 WDR54

6 ENSG00000006740 ARHGAP44

6 ENSG00000006837 CDKL3

6 ENSG00000007062 PROM1

6 ENSG00000007174 DNAH9

6 ENSG00000007237 GAS7

6 ENSG00000007384 RHBDF1

6 ENSG00000007866 TEAD3

6 ENSG00000008083 JARID2

6 ENSG00000010361 FUZ

6 ENSG00000010626 LRRC23

6 ENSG00000011143 MKS1

6 ENSG00000011295 TTC19

6 ENSG00000011485 PPP5C

6 ENSG00000016402 IL20RA

6 ENSG00000016864 GLT8D1

6 ENSG00000021300 PLEKHB1

6 ENSG00000021645 NRXN3

6 ENSG00000024862 CCDC28A

6 ENSG00000025156 HSF2

6 ENSG00000025772 TOMM34

6 ENSG00000026508 CD44

6 ENSG00000032742 IFT88

6 ENSG00000034239 EFCAB1

6 ENSG00000036672 USP2

6 ENSG00000037474 NSUN2

6 ENSG00000039139 DNAH5

6 ENSG00000042317 SPATA7

6 ENSG00000043514 TRIT1

6 ENSG00000048342 CC2D2A

6 ENSG00000048471 SNX29

6 ENSG00000048991 R3HDM1

6 ENSG00000049319 SRD5A2

6 ENSG00000049759 NEDD4L

6 ENSG00000049769 PPP1R3F

6 ENSG00000050327 ARHGEF5

6 ENSG00000051341 POLQ

6 ENSG00000054219 LY75

6 ENSG00000054282 SDCCAG8

6 ENSG00000054392 HHAT

6 ENSG00000054983 GALC

6 ENSG00000056998 GYG2

6 ENSG00000057019 DCBLD2

6 ENSG00000058085 LAMC2

6 ENSG00000064199 SPA17

6 ENSG00000064692 SNCAIP

6 ENSG00000064999 ANKS1A

6 ENSG00000065357 DGKA

6 ENSG00000065491 TBC1D22B

6 ENSG00000065970 FOXJ2

6 ENSG00000066084 DIP2B

6 ENSG00000066185 ZMYND12

6 ENSG00000066248 NGEF

6 ENSG00000066629 EML1

6 ENSG00000067208 EVI5

6 ENSG00000067369 TP53BP1

6 ENSG00000068650 ATP11A

6 ENSG00000068885 IFT80

6 ENSG00000068971 PPP2R5B

6 ENSG00000070444 MNT

6 ENSG00000070718 AP3M2

6 ENSG00000070731 ST6GALNAC2

6 ENSG00000070761 C16orf80

6 ENSG00000071539 TRIP13

6 ENSG00000072133 RPS6KA6

6 ENSG00000072422 RHOBTB1

6 ENSG00000073050 XRCC1

6 ENSG00000073464 CLCN4

6 ENSG00000074621 SLC24A1

6 ENSG00000074964 ARHGEF10L

6 ENSG00000075142 SRI

6 ENSG00000075240 GRAMD4

6 ENSG00000075568 TMEM131

6 ENSG00000075945 KIFAP3

6 ENSG00000077327 SPAG6

6 ENSG00000077514 POLD3

6 ENSG00000077800 FKBP6

6 ENSG00000078246 TULP3

6 ENSG00000078487 ZCWPW1

6 ENSG00000078900 TP73

6 ENSG00000079156 OSBPL6

6 ENSG00000079335 CDC14A

6 ENSG00000080298 RFX3

6 ENSG00000080572 PIH1D3

6 ENSG00000080824 HSP90AA1

6 ENSG00000081870 HSPB11

6 ENSG00000083290 ULK2

6 ENSG00000084764 MAPRE3

6 ENSG00000085063 CD59

6 ENSG00000085433 WDR47

6 ENSG00000086102 NFX1

6 ENSG00000086200 IPO11

6 ENSG00000087053 MTMR2

6 ENSG00000087152 ATXN7L3

6 ENSG00000087365 SF3B2

6 ENSG00000087510 TFAP2C

6 ENSG00000087903 RFX2

6 ENSG00000088053 GP6

6 ENSG00000088320 REM1

6 ENSG00000088727 KIF9

6 ENSG00000088833 NSFL1C

6 ENSG00000088970 PLK1S1

6 ENSG000000888986 DYNLL1

6 ENSG00000089060 SLC8B1

6 ENSG00000089091 DZANK1

6 ENSG00000089101 C20orf26

6 ENSG00000089123 TASP1

6 ENSG00000090273 NUDC

6 ENSG00000090661 CERS4

6 ENSG00000090971 NAT14

6 ENSG00000091181 IL5RA

6 ENSG00000092850 TEKT2

6 ENSG00000095261 PSMD5

6 ENSG00000095319 NUP188

6 ENSG00000096433 ITPR3

6 ENSG00000096872 IFT74

6 ENSG00000100012 SEC14L3

6 ENSG00000100124 ANKRD54

6 ENSG00000100162 CENPM

6 ENSG00000100211 CBY1

6 ENSG00000100218 RTDR1

6 ENSG00000100228 RAB36

6 ENSG00000100271 TTLL1

6 ENSG00000100294 MCAT

6 ENSG00000100345 MYH9

6 ENSG00000100418 DESI1

6 ENSG00000100422 CERK

6 ENSG00000100441 KHNYN

6 ENSG00000100462 PRMT5

6 ENSG00000100490 CDKL1

6 ENSG00000100583 SAMD15

6 ENSG00000100591 AHSA1

6 ENSG00000100625 SIX4

6 ENSG00000100784 RPS6KA5

6 ENSG00000101052 IFT52

6 ENSG00000101222 SPEF1

6 ENSG00000101448 EPPIN

6 ENSG00000101928 MOSPD1

6 ENSG00000102048 ASB9

6 ENSG00000102230 PCYT1B

6 ENSG00000102349 KLF8

6 ENSG00000102466 FGF14

6 ENSG00000102543 CDADC1

6 ENSG00000102738 MRPS31

6 ENSG00000102743 SLC25A15

6 ENSG00000102781 KATNAL1

6 ENSG00000102886 GDPD3

6 ENSG00000102996 MMP15

6 ENSG00000103021 CCDC113

6 ENSG00000103042 SLC38A7

6 ENSG00000103160 HSDL1

6 ENSG00000103174 NAGPA

6 ENSG00000103194 USP10

6 ENSG00000103260 METRN

6 ENSG00000103351 CLUAP1

6 ENSG00000103494 RPGRIP1L

6 ENSG00000103540 CCP110

6 ENSG00000103599 IQCH

6 ENSG00000103647 CORO2B

6 ENSG00000103740 ACSBG1

6 ENSG00000103994 ZNF106

6 ENSG00000103995 CEP152

6 ENSG00000104237 RP1

6 ENSG00000104361 NIPAL2

6 ENSG00000104427 ZC2HC1A

6 ENSG00000104472 CHRAC1

6 ENSG00000104490 NCALD

6 ENSG00000104549 SQLE

6 ENSG00000104723 TUSC3

6 ENSG00000105258 POLR2I

6 ENSG00000105278 ZFR2

6 ENSG00000105519 CAPS

6 ENSG00000105948 TTC26

6 ENSG00000105982 RNF32

6 ENSG00000106012 IQCE

6 ENSG00000106049 HIBADH

6 ENSG00000106052 TAX1BP1

6 ENSG00000106125 FAM188B

6 ENSG00000106399 RPA3

6 ENSG00000106459 NRF1

6 ENSG00000106477 CEP41

6 ENSG00000106701 FSD1L

6 ENSG00000106992 AK1

6 ENSG00000107185 RGP1

6 ENSG00000107186 MPDZ

6 ENSG00000107249 GLIS3

6 ENSG00000107521 HPS1

6 ENSG00000107816 LZTS2

6 ENSG00000107957 SH3PXD2A

6 ENSG00000108187 PBLD

6 ENSG00000108395 TRIM37

6 ENSG00000108406 DHX40

6 ENSG00000108479 GALK1

6 ENSG00000108641 B9D1

6 ENSG00000108733 PEX12

6 ENSG00000108753 HNF1B

6 ENSG00000108819 PPP1R9B

6 ENSG00000108946 PRKAR1A

6 ENSG00000108947 EFNB3

6 ENSG00000109083 IFT20

6 ENSG00000109171 SLAIN2

6 ENSG00000109501 WFS1

6 ENSG00000109680 TBC1D19

6 ENSG00000109685 WHSC1

6 ENSG00000109762 SNX25

6 ENSG00000109771 LRP2BP

6 ENSG00000109944 C11orf63

6 ENSG00000110025 SNX15

6 ENSG00000110318 KIAA1377

6 ENSG00000110841 PPFIBP1

6 ENSG00000111145 ELK3

6 ENSG00000111218 PRMT8

6 ENSG00000111254 AKAP3

6 ENSG00000111262 KCNA1

6 ENSG00000111321 LTBR

6 ENSG00000111325 OGFOD2

6 ENSG00000111450 STX2

6 ENSG00000111554 MDM1

6 ENSG00000111647 UHRF1BP1L

6 ENSG00000111674 ENO2

6 ENSG00000111728 ST8SIA1

6 ENSG00000111834 RSPH4A

6 ENSG00000111837 MAK

6 ENSG00000111877 MCM9

6 ENSG00000111879 FAM184A

6 ENSG00000111907 TPD52L1

6 ENSG00000111961 SASH1

6 ENSG00000112183 RBM24

6 ENSG00000112186 CAP2

6 ENSG00000112530 PACRG

6 ENSG00000112539 C6orf118

6 ENSG00000112559 MDFI

6 ENSG00000112584 FAM120B

6 ENSG00000112667 DNPH1

6 ENSG00000112796 ENPP5

6 ENSG00000112981 NME5

6 ENSG00000113141 IK

6 ENSG00000113318 MSH3

6 ENSG00000113456 RAD1

6 ENSG00000113583 C5orf15

6 ENSG00000113645 WWC1

6 ENSG00000113946 CLDN16

6 ENSG00000113966 ARL6

6 ENSG00000114446 IFT57

6 ENSG00000114455 HHLA2

6 ENSG00000114473 IQCG

6 ENSG00000114656 KIAA1257

6 ENSG00000114670 NEK11

6 ENSG00000114805 PLCH1

6 ENSG00000114904 NEK4

6 ENSG00000115107 STEAP3

6 ENSG00000115145 STAM2

6 ENSG00000115216 NRBP1

6 ENSG00000115423 DNAH6

6 ENSG00000115425 PECR

6 ENSG00000115486 GGCX

6 ENSG00000115685 PPP1R7

6 ENSG00000115750 TAF1B

6 ENSG00000115947 ORC4

6 ENSG00000115970 THADA

6 ENSG00000115998 C2orf42

6 ENSG00000116032 GRIN3B

6 ENSG00000116127 ALMS1

6 ENSG00000116128 BCL9

6 ENSG00000116525 TRIM62

6 ENSG00000116675 DNAJC6

6 ENSG00000116793 PHTF1

6 ENSG00000116885 OSCP1

6 ENSG00000116957 TBCE

6 ENSG00000117016 RIMS3

6 ENSG00000117477 CCDC181

6 ENSG00000117602 RCAN3

6 ENSG00000118096 IFT46

6 ENSG00000118307 CASC1

6 ENSG00000118407 FILIP1

6 ENSG00000118418 HMGN3

6 ENSG00000118420 UBE3D

6 ENSG00000118690 ARMC2

6 ENSG00000118965 WDR35

6 ENSG00000118997 DNAH7

6 ENSG00000119147 C2orf40

6 ENSG00000119328 FAM206A

6 ENSG00000119333 WDR34

6 ENSG00000119397 CNTRL

6 ENSG00000119401 TRIM32

6 ENSG00000119402 FBXW2

6 ENSG00000119636 CCDC176

6 ENSG00000119640 ACYP1

6 ENSG00000119650 IFT43

6 ENSG00000119661 DNAL1

6 ENSG00000119685 TTLL5

6 ENSG00000119689 DLST

6 ENSG00000119698 PPP4R4

6 ENSG00000119703 ZC2HC1C

6 ENSG00000119782 FKBP1B

6 ENSG00000120051 CCDC147

6 ENSG00000120055 C10orf95

6 ENSG00000120256 LRP11

6 ENSG00000120262 CCDC170

6 ENSG00000120279 MYCT1

6 ENSG00000120306 CYSTM1

6 ENSG00000120658 ENOX1

6 ENSG00000120685 PROSER1

6 ENSG00000120694 HSPH1

6 ENSG00000121057 AKAP1

6 ENSG00000121413 ZSCAN18

6 ENSG00000121486 TRMT1L

6 ENSG00000121671 CRY2

6 ENSG00000122376 FAM35A

6 ENSG00000122507 BBS9

6 ENSG00000122970 IFT81

6 ENSG00000123607 TTC21B

6 ENSG00000123810 B9D2

6 ENSG00000123977 DAW1

6 ENSG00000124074 ENKD1

6 ENSG00000124237 C20orf85

6 ENSG00000124678 TCP11

6 ENSG00000124749 COL21A1

6 ENSG00000125124 BBS2

6 ENSG00000125384 PTGER2

6 ENSG00000125409 TEKT3

6 ENSG00000125482 TTF1

6 ENSG00000125531 C20orf195

6 ENSG00000125733 TRIP10

6 ENSG00000125779 PANK2

6 ENSG00000125871 MGME1

6 ENSG00000125968 ID1

6 ENSG00000125991 ERGIC3

6 ENSG00000126107 HECTD3

6 ENSG00000126391 FRMD8

6 ENSG00000126432 PRDX5

6 ENSG00000126773 PCNXL4

6 ENSG00000126777 KTN1

6 ENSG00000126778 SIX1

6 ENSG00000126870 WDR60

6 ENSG00000127399 LRRC61

6 ENSG00000127824 TUBA4A

6 ENSG00000127863 TNFRSF19

6 ENSG00000127914 AKAP9

6 ENSG00000127952 STYXL1

6 ENSG00000128346 C22orf23

6 ENSG00000128408 RIBC2

6 ENSG00000128536 CDHR3

6 ENSG00000128581 RABL5

6 ENSG00000128607 KLHDC10

6 ENSG00000128881 TTBK2

6 ENSG00000128891 C15orf57

6 ENSG00000129007 CALML4

6 ENSG00000129028 THAP10

6 ENSG00000129151 BBOX1

6 ENSG00000129295 LRRC6

6 ENSG00000129521 EGLN3

6 ENSG00000129654 FOXJ1

6 ENSG00000129951

6 ENSG00000130177 CDC16

6 ENSG00000130363 RSPH3

6 ENSG00000130413 STK33

6 ENSG00000130433 CACNG6

6 ENSG00000130511 SSBP4

6 ENSG00000130560 UBAC1

6 ENSG00000130640 TUBGCP2

6 ENSG00000130762 ARHGEF16

6 ENSG00000130770 ATPIF1

6 ENSG00000130962 PRRG1

6 ENSG00000131437 KIF3A

6 ENSG00000131470 PSMC3IP

6 ENSG00000131697 NPHP4

6 ENSG00000131711 MAP1B

6 ENSG00000131828 PDHA1

6 ENSG00000131848 ZSCAN5A

6 ENSG00000131941 RHPN2

6 ENSG00000131969 ABHD12B

6 ENSG00000132003 ZSWIM4

6 ENSG00000132004 FBXW9

6 ENSG00000132010 ZNF20

6 ENSG00000132122 SPATA6

6 ENSG00000132139 GAS2L2

6 ENSG00000132259 CNGA4

6 ENSG00000132321 IQCA1

6 ENSG00000132549 VPS13B

6 ENSG00000132554 RGS22

6 ENSG00000132640 BTBD3

6 ENSG00000132664 POLR3F

6 ENSG00000132768 DPH2

6 ENSG00000133056 PIK3C2B

6 ENSG00000133065 SLC41A1

6 ENSG00000133104 SPG20

6 ENSG00000133115 STOML3

6 ENSG00000133131 MORC4

6 ENSG00000133216 EPHB2

6 ENSG00000133256 PDE6B

6 ENSG00000133488 SEC14L4

6 ENSG00000133627 ACTR3B

6 ENSG00000133640 LRRIQ1

6 ENSG00000133678 TMEM254

6 ENSG00000133739 LRRCC1

6 ENSG00000133958 UNC79

6 ENSG00000134138 MEIS2

6 ENSG00000134247 PTGFRN

6 ENSG00000135070 ISCA1

6 ENSG00000135205 CCDC146

6 ENSG00000135245 HILPDA

6 ENSG00000135315 KIAA1009

6 ENSG00000135338 LCA5

6 ENSG00000135406 PRPH

6 ENSG00000135519 KCNH3

6 ENSG00000135535 CD164

6 ENSG00000135537 LACE1

6 ENSG00000135549 PKIB

6 ENSG00000135597 REPS1

6 ENSG00000135931 ARMC9

6 ENSG00000135951 TSGA10

6 ENSG00000135966 TGFBRAP1

6 ENSG00000136044 APPL2

6 ENSG00000136319 TTC5

6 ENSG00000136448 NMT1

6 ENSG00000136449 MYCBPAP

6 ENSG00000136451 VEZF1

6 ENSG00000136715 SAP130

6 ENSG00000136811 ODF2

6 ENSG00000136918 WDR38

6 ENSG00000137266 SLC22A23

6 ENSG00000137274 BPHL

6 ENSG00000137414 FAM8A1

6 ENSG00000137434 C6orf52

6 ENSG00000137473 TTC29

6 ENSG00000137494 ANKRD42

6 ENSG00000137601 NEK1

6 ENSG00000137691 C11orf70

6 ENSG00000137707 BTG4

6 ENSG00000137819 PAQR5

6 ENSG00000137821 LRRC49

6 ENSG00000137960 GIPC2

6 ENSG00000138002 IFT172

6 ENSG00000138036 DYNC2LI1

6 ENSG00000138041 SMEK2

6 ENSG00000138175 ARL3

6 ENSG00000138400 MDH1B

6 ENSG00000138433 CIR1

6 ENSG00000138443 ABI2

6 ENSG00000138587 MNS1

6 ENSG00000138622 HCN4

6 ENSG00000138640 FAM13A

6 ENSG00000138670 RASGEF1B

6 ENSG00000138769 CDKL2

6 ENSG00000138771 SHROOM3

6 ENSG00000138823 MTTP

6 ENSG00000139537 CCDC65

6 ENSG00000139624 CERS5

6 ENSG00000139714 MORN3

6 ENSG00000139971 C14orf37

6 ENSG00000139974 SLC38A6

6 ENSG00000140025 EFCAB11

6 ENSG00000140043 PTGR2

6 ENSG00000140057 AK7

6 ENSG00000140284 SLC27A2

6 ENSG00000140403 DNAJA4

6 ENSG00000140463 BBS4

6 ENSG00000140481 CCDC33

6 ENSG00000140527 WDR93

6 ENSG00000140564 FURIN

6 ENSG00000140600 SH3GL3

6 ENSG00000140632 GLYR1

6 ENSG00000140876 NUDT7

6 ENSG00000141012 GALNS

6 ENSG00000141013 GAS8

6 ENSG00000141098 GFOD2

6 ENSG00000141294 LRRC46

6 ENSG00000141376 BCAS3

6 ENSG00000141499 WRAP53

6 ENSG00000141510 TP53

6 ENSG00000141580 WDR45B

6 ENSG00000141665 FBXO15

6 ENSG00000142621 FHAD1

6 ENSG00000142655 PEX14

6 ENSG00000142677 IL22RA1

6 ENSG00000143093 STRIP1

6 ENSG00000143156 NME7

6 ENSG00000143179 UCK2

6 ENSG00000143222 UFC1

6 ENSG00000143258 USP21

6 ENSG00000143479 DYRK3

6 ENSG00000143499 SMYD2

6 ENSG00000143537 ADAM15

6 ENSG00000143595 AQP10

6 ENSG00000143633 C1orf131

6 ENSG00000143653 SCCPDH

6 ENSG00000143786 CNIH3

6 ENSG00000143933 CALM2

6 ENSG00000143951 WDPCP

6 ENSG00000144061 NPHP1

6 ENSG00000144233 AMMECR1L

6 ENSG00000144451 SPAG16

6 ENSG00000144504 ANKMY1

6 ENSG00000145075 CCDC39

6 ENSG00000145331 TRMT10A

6 ENSG00000145414 NAF1

6 ENSG00000145491 ROPN1L

6 ENSG00000145945 FAM50B

6 ENSG00000145982 FARS2

6 ENSG00000146038 DCDC2

6 ENSG00000146083 RNF44

6 ENSG00000146221 TCTE1

6 ENSG000001146233 CYP39A1

6 ENSG00000146242 TPBG

6 ENSG00000146243 IRAK1BP1

6 ENSG00000146376 ARHGAP18

6 ENSG00000146722

6 ENSG00000146729 GBAS

6 ENSG00000146733 PSPH

6 ENSG00000146856 AGBL3

6 ENSG00000147003 TMEM27

6 ENSG00000147117 ZNF157

6 ENSG00000147202 DIAPH2

6 ENSG00000147224 PRPS1

6 ENSG00000147231 CXorf57

6 ENSG00000147316 MCPH1

6 ENSG00000147400 CETN2

6 ENSG00000147457 CHMP7

6 ENSG00000147894 C9orf72

6 ENSG00000148057 IDNK

6 ENSG00000148219 ASTN2

6 ENSG00000148225 WDR31

6 ENSG00000148660 CAMK2G

6 ENSG00000148814 LRRC27

6 ENSG00000148842 CNNM2

6 ENSG00000149050 ZNF214

6 ENSG00000149179 C11orf49

6 ENSG00000149201 CCDC81

6 ENSG00000149292 TTC12

6 ENSG00000149300 C11orf52

6 ENSG00000149328 GLB1L2

6 ENSG00000149480 MTA2

6 ENSG00000149573 MPZL2

6 ENSG00000149782 PLCB3

6 ENSG00000150281 CTF1

6 ENSG00000150433 TMEM218

6 ENSG00000150456 N6AMT2

6 ENSG00000150628 SPATA4

6 ENSG00000150667 FSIP1

6 ENSG00000150764 DIXDC1

6 ENSG00000150773 PIH1D2

6 ENSG00000150873 C2orf50

6 ENSG00000151023 ENKUR

6 ENSG00000151065 DCP1B

6 ENSG00000151320 AKAP6

6 ENSG00000151338 MIPOL1

6 ENSG00000151413 NUBPL

6 ENSG00000151445 VIPAS39

6 ENSG00000151575 TEX9

6 ENSG00000151689 INPP1

6 ENSG00000151773 CCDC122

6 ENSG00000151779 NBAS

6 ENSG00000152076 CCDC74B

6 ENSG00000152464 RPP38

6 ENSG00000152503 TRIM36

6 ENSG00000152582 SPEF2

6 ENSG00000152611 CAPSL

6 ENSG00000152763 WDR78

6 ENSG00000152936 IFLTD1

6 ENSG00000153132 CLGN

6 ENSG00000153140 CETN3

6 ENSG00000153237 CCDC148

6 ENSG00000153347 FAM81B

6 ENSG00000153531 ADPRHL1

6 ENSG00000153558 FBXL2

6 ENSG00000153560 UBP1

6 ENSG00000153714 LURAP1L

6 ENSG00000153774 CFDP1

6 ENSG00000153789 FAM92B

6 ENSG00000153832 FBXO36

6 ENSG00000153896 ZNF599

6 ENSG00000153904 DDAH1

6 ENSG00000153930 ANKFN1

6 ENSG00000154124 FAM105B

6 ENSG00000154153 FAM134B

6 ENSG00000154240 CEP112

6 ENSG00000154380 ENAH

6 ENSG00000154479 CCDC173

6 ENSG00000154556 SORBS2

6 ENSG00000154760 SLFN13

6 ENSG00000154917 RAB6B

6 ENSG00000154930 ACSS1

6 ENSG00000155026 RSPH10B

6 ENSG00000155085 AK9

6 ENSG00000155096 AZIN1

6 ENSG00000155189 AGPAT5

6 ENSG00000155530 LRGUK

6 ENSG00000155666 KDM8

6 ENSG00000155749 ALS2CR12

6 ENSG00000155761 SPAG17

6 ENSG00000155816 FMN2

6 ENSG00000155974 GRIP1

6 ENSG00000156030 ELMSAN1

6 ENSG00000156049 GNA14

6 ENSG00000156050 FAM161B

6 ENSG00000156171 DRAM2

6 ENSG00000156172 C8orf37

6 ENSG00000156206 C15orf26

6 ENSG00000156232 WHAMM

6 ENSG00000156299 TIAM1

6 ENSG00000156313 RPGR

6 ENSG00000156463 SH3RF2

6 ENSG00000156958 GALK2

6 ENSG00000157227 MMP14

6 ENSG00000157330 C1orf158

6 ENSG00000157423 HYDIN

6 ENSG00000157429 ZNF19

6 ENSG00000157470 FAM81A

6 ENSG00000157538 DSCR3

6 ENSG00000157578 LCA5L

6 ENSG00000157653 C9orf43

6 ENSG00000157796 WDR19

6 ENSG00000157856 DRC1

6 ENSG00000157869 RAB28

6 ENSG00000158023 WDR66

6 ENSG00000158113 LRRC43

6 ENSG00000158122 AAED1

6 ENSG00000158234 FAIM

6 ENSG00000158296 SLC13A3

6 ENSG00000158423 RIBC1

6 ENSG00000158428 C2orf62

6 ENSG00000158445 KCNB1

6 ENSG00000158486 DNAH3

6 ENSG00000158669 AGPAT6

6 ENSG00000158850 B4GALT3

6 ENSG00000159079 C21orf59

6 ENSG00000159239 C2orf81

6 ENSG00000159685 CHCHD6

6 ENSG00000159713 TPPP3

6 ENSG00000159714 ZDHHC1

6 ENSG00000160051 IQCC

6 ENSG00000160145 KALRN

6 ENSG00000160183 TMPRSS3

6 ENSG00000160188 RSPH1

6 ENSG00000160345 C9orf116

6 ENSG00000160613 PCSK7

6 ENSG00000160753 RUSC1

6 ENSG00000160803 UBQLN4

6 ENSG00000160949 TONSL

6 ENSG00000160991 ORAI2

6 ENSG00000161036 LRWD1

6 ENSG00000161040 FBXL13

6 ENSG00000161326 DUSP14

6 ENSG00000161328 LRRC56

6 ENSG00000161513 FDXR

6 ENSG00000161905 ALOX15

6 ENSG00000162040 HS3ST6

6 ENSG00000162105 SHANK2

6 ENSG00000162148 PPP1R32

6 ENSG00000162302 RPS6KA4

6 ENSG00000162543 UBXN10

6 ENSG00000162598 C1orf87

6 ENSG00000162600 OMA1

6 ENSG00000162616 DNAJB4

6 ENSG00000162620 LRRIQ3

6 ENSG00000162643 WDR63

6 ENSG00000162755 KLHDC9

6 ENSG00000162769 FLVCR1

6 ENSG00000162814 SPATA17

6 ENSG00000162999 DUSP19

6 ENSG00000163001 CCDC104

6 ENSG00000163006 CCDC138

6 ENSG00000163040 CCDC74A

6 ENSG00000163060 TEKT4

6 ENSG00000163071 SPATA18

6 ENSG00000163075

6 ENSG00000163083 INHBB

6 ENSG00000163093 BBS5

6 ENSG00000163125 RPRD2

6 ENSG00000163138 PACRGL

6 ENSG00000163214 DHX57

6 ENSG00000163251 FZD5

6 ENSG00000163263 C1orf189

6 ENSG00000163322 FAM175A

6 ENSG00000163349 HIPK1

6 ENSG00000163491 NEK10

6 ENSG00000163512 AZI2

6 ENSG00000163521 GLB1L

6 ENSG00000163576 EFHB

6 ENSG00000163596 ICA1L

6 ENSG00000163617 KIAA1407

6 ENSG00000163624 CDS1

6 ENSG00000163655 GMPS

6 ENSG00000163686 ABHD6

6 ENSG00000163818 LZTFL1

6 ENSG00000163875 MEAF6

6 ENSG00000163879 DNALI1

6 ENSG00000164002 EXO5

6 ENSG00000164099 PRSS12

6 ENSG00000164114 MAP9

6 ENSG00000164118 CEP44

6 ENSG00000164185 ZNF474

6 ENSG00000164306 PRIMPOL

6 ENSG00000164402 8-Sep

6 ENSG00000164404 GDF9

6 ENSG00000164411 GJB7

6 ENSG00000164440 TXLNB

6 ENSG00000164465 DCBLD1

6 ENSG00000164542 KIAA0895

6 ENSG00000164627 KIF6

6 ENSG00000164674 SYTL3

6 ENSG00000164675 IQUB

6 ENSG00000164746 C7orf57

6 ENSG00000164758 MED30

6 ENSG00000164818 HEATR2

6 ENSG00000164938 TP53INP1

6 ENSG00000164953 TMEM67

6 ENSG00000164970 FAM219A

6 ENSG00000164972 C9orf24

6 ENSG00000165029 ABCA1

6 ENSG00000165084 C8orf34

6 ENSG00000165097 KDM1B

6 ENSG00000165118 C9orf64

6 ENSG00000165124 SVEP1

6 ENSG00000165164 CXorf22

6 ENSG00000165185 KIAA1958

6 ENSG00000165209 STRBP

6 ENSG00000165219 GAPVD1

6 ENSG00000165309 ARMC3

6 ENSG00000165383 LRRC18

6 ENSG00000165506 DNAAF2

6 ENSG00000165533 TTC8

6 ENSG00000165695 AK8

6 ENSG00000165698 C9orf9

6 ENSG00000165724 ZMYND19

6 ENSG00000165730 STOX1

6 ENSG00000165807 PPP1R36

6 ENSG00000166165 CKB

6 ENSG00000166171 DPCD

6 ENSG00000166173 LARP6

6 ENSG00000166246 C16orf71

6 ENSG00000166262 FAM227B

6 ENSG00000166263 STXBP4

6 ENSG00000166275 C10orf32

6 ENSG00000166311 SMPD1

6 ENSG00000166313 APBB1

6 ENSG00000166323 C11orf65

6 ENSG00000166352 C11orf74

6 ENSG00000166402 TUB

6 ENSG00000166435 XRRA1

6 ENSG00000166455 C16orf46

6 ENSG00000166526 ZNF3

6 ENSG00000166578 IQCD

6 ENSG00000166592 RRAD

6 ENSG00000166596 WDR16

6 ENSG00000166946 CCNDBP1

6 ENSG00000166959 MS4A8

6 ENSG00000166963 MAP1A

6 ENSG00000167065 DUSP18

6 ENSG00000167094 TTC16

6 ENSG00000167113 COQ4

6 ENSG00000167131 CCDC103

6 ENSG00000167136 ENDOG

6 ENSG00000167186 COQ7

6 ENSG00000167216 KATNAL2

6 ENSG00000167523 SPATA33

6 ENSG00000167550 RHEBL1

6 ENSG00000167552 TUBA1A

6 ENSG00000167646 DNAAF3

6 ENSG00000167733 HSD11B1L

6 ENSG00000167740 CYB5D2

6 ENSG00000167858 TEKT1

6 ENSG00000167904 TMEM68

6 ENSG00000167962 ZNF598

6 ENSG00000168014 C2CD3

6 ENSG00000168038 ULK4

6 ENSG00000168314 MOBP

6 ENSG00000168350 DEGS2

6 ENSG00000168487 BMP1

6 ENSG00000168575 SLC20A2

6 ENSG00000168589 DYNLRB2

6 ENSG00000168658 VWA3B

6 ENSG00000168675 LDLRAD4

6 ENSG00000168734 PKIG

6 ENSG00000168754 FAM178B

6 ENSG00000168772 CXXC4

6 ENSG00000168778 TCTN2

6 ENSG00000168884 TNIP2

6 ENSG00000168938 PPIC

6 ENSG00000169064 ZBBX

6 ENSG00000169126 ARMC4

6 ENSG00000169189 NSMCE1

6 ENSG00000169213 RAB3B

6 ENSG00000169379 ARL13B

6 ENSG00000169550 MUC15

6 ENSG00000169902 TPST1

6 ENSG00000169905 TOR1AIP2

6 ENSG00000170231 FABP6

6 ENSG00000170264 FAM161A

6 ENSG00000170270 C14orf142

6 ENSG00000170469 SPATA24

6 ENSG00000170482 SLC23A1

6 ENSG00000170509 HSD17B13

6 ENSG00000170871 KIAA0232

6 ENSG00000170959 DCDC1

6 ENSG00000171132 PRKCE

6 ENSG00000171160 MORN4

6 ENSG00000171174 RBKS

6 ENSG00000171428 NAT1

6 ENSG00000171517 LPAR3

6 ENSG00000171533 MAP6

6 ENSG00000171574 ZNF584

6 ENSG00000171595 DNAI2

6 ENSG00000171757 LRRC34

6 ENSG00000171793 CTPS1

6 ENSG00000171798 KNDC1

6 ENSG00000171885 AQP4

6 ENSG00000171962 LRRC48

6 ENSG00000172164 SNTB1

6 ENSG000001172301 COPRS

6 ENSG00000172361 CCDC11

6 ENSG00000172426 RSPH9

6 ENSG00000172578 KLHL6

6 ENSG00000172671 ZFAND4

6 ENSG00000172955 ADH6

6 ENSG00000173013 CCDC96

6 ENSG00000173208 ABCD2

6 ENSG00000173226 IQCB1

6 ENSG00000173627 APOBEC4

6 ENSG00000173838 10-Mar

6 ENSG00000173947 PIFO

6 ENSG00000174007 CEP19

6 ENSG00000174132 FAM174A

6 ENSG00000174156 GSTA3

6 ENSG00000174343 CHRNA9

6 ENSG00000174456 C12orf76

6 ENSG00000174483 BBS1

6 ENSG00000174586 ZNF497

6 ENSG00000174628 IQCK

6 ENSG00000174705 SH3PXD2B

6 ENSG00000174776 WDR49

6 ENSG00000174796 THAP6

6 ENSG00000174808 BTC

6 ENSG00000174898 CATSPERD

6 ENSG00000175279 APITD1

6 ENSG00000175376 EIF1AD

6 ENSG00000175664 TEX26

6 ENSG00000175697 GPR156

6 ENSG00000175792 RUVBL1

6 ENSG00000175970 UNC119B

6 ENSG00000176040 TMPRSS7

6 ENSG00000176171 BNIP3

6 ENSG00000176209 SMIM19

6 ENSG00000176381 PRR18

6 ENSG00000176401 EID2B

6 ENSG00000176485 PLA2G16

6 ENSG00000176563 CNTD1

6 ENSG00000176601 MAP3K19

6 ENSG00000176714 CCDC121

6 ENSG00000176986 SEC24C

6 ENSG00000177103 DSCAML1

6 ENSG00000177112 MRVI1-AS1

6 ENSG00000177398 UMODL1

6 ENSG00000177459 C8orf47

6 ENSG00000177508 IRX3

6 ENSG00000177640 CASC2

6 ENSG00000177674 AGTRAP

6 ENSG00000177994 C2orf73

6 ENSG00000178053 MLF1

6 ENSG00000178075 GRAMD1C

6 ENSG00000178125 PPP1R42

6 ENSG00000178149 DALRD3

6 ENSG00000178425 NT5DC1

6 ENSG00000178460 MCMDC2

6 ENSG00000178467 P4HTM

6 ENSG00000178568 ERBB4

6 ENSG00000178665 ZNF713

6 ENSG00000178732 GP5

6 ENSG00000178796 RIIAD1

6 ENSG00000178965 C1orf173

6 ENSG00000179029 TMEM107

6 ENSG00000179071 CCDC89

6 ENSG00000179133 C10orf67

6 ENSG00000179195 ZNF664

6 ENSG00000179240

6 ENSG00000179598 PLD6

6 ENSG00000179813 FAM216B

6 ENSG00000179902 C1orf194

6 ENSG00000180098 TRNAU1AP

6 ENSG00000180263 FGD6

6 ENSG00000180346 TIGD2

6 ENSG00000180481 GLIPR1L2

6 ENSG00000180509 KCNE1

6 ENSG00000180769 WDFY3-AS2

6 ENSG00000180787 ZFP3

6 ENSG00000180914 OXTR

6 ENSG00000181004 BBS12

6 ENSG00000181322 NME9

6 ENSG00000181481 RNF135

6 ENSG00000181619 GPR135

6 ENSG00000182093 WRB

6 ENSG00000182224 CYB5D1

6 ENSG00000182329

6 ENSG00000182504 CEP97

6 ENSG00000182518 FAM104B

6 ENSG00000182768 NGRN

6 ENSG00000182957 SPATA13

6 ENSG00000183117 CSMD1

6 ENSG00000183161 FANCF

6 ENSG00000183207 RUVBL2

6 ENSG00000183273 CCDC60

6 ENSG00000183323 CCDC125

6 ENSG00000183346 C10orf107

6 ENSG00000183578 TNFAIP8L3

6 ENSG00000183628 DGCR6

6 ENSG00000183644 C11orf88

6 ENSG00000183690 EFHC2

6 ENSG00000183784 C9orf66

6 ENSG00000183826 BTBD9

6 ENSG00000183831 ANKRD45

6 ENSG00000183914 DNAH2

6 ENSG00000183941 HIST2H4A

6 ENSG00000184154 LRTOMT

6 ENSG00000184349 EFNA5

6 ENSG00000184385 C21orf128

6 ENSG00000184500 PROS1

6 ENSG00000184613 NELL2

6 ENSG00000184702 5-Sep

6 ENSG00000184731 FAM110C

6 ENSG00000184886 PIGW

6 ENSG00000184898 RBM43

6 ENSG00000184939 ZFP90

6 ENSG00000184986 TMEM121

6 ENSG00000185055 EFCAB10

6 ENSG00000185158 LRRC37B

6 ENSG00000185220 PGBD2

6 ENSG00000185222 WBP5

6 ENSG00000185250 PPIL6

6 ENSG00000185261 KIAA0825

6 ENSG00000185267 CDNF

6 ENSG00000185305 ARL15

6 ENSG00000185361 TNFAIP8L1

6 ENSG00000185379 RAD51D

6 ENSG00000185420 SMYD3

6 ENSG00000185608 MRPL40

6 ENSG00000185681 MORN5

6 ENSG00000185875 THNSL1

6 ENSG00000185989 RASA3

6 ENSG00000186094 AGBL4

6 ENSG00000186104 CYP2R1

6 ENSG00000186132 C2orf76

6 ENSG00000186198 SLC51B

6 ENSG00000186231 KLHL32

6 ENSG00000186314 PRELID2

6 ENSG00000186329 TMEM212

6 ENSG00000186352 ANKRD37

6 ENSG00000186471 AKAP14

6 ENSG00000186496 ZNF396

6 ENSG00000186523 FAM86B1

6 ENSG00000186625 KATNA1

6 ENSG00000186638 KIF24

6 ENSG00000186687 LYRM7

6 ENSG00000186889 TMEM17

6 ENSG00000186952 TMEM232

6 ENSG00000186973 FAM183A

6 ENSG00000186976 EFCAB6

6 ENSG00000187079 TEAD1

6 ENSG00000187122 SLIT1

6 ENSG00000187189 TSPYL4

6 ENSG00000187240 DYNC2H1

6 ENSG00000187260 WDR86

6 ENSG00000187535 IFT140

6 ENSG00000187624 C17orf97

6 ENSG00000187642 C1orf170

6 ENSG00000187695

6 ENSG00000187726 DNAJB13

6 ENSG00000187733 AMY1C

6 ENSG00000188010 MORN2

6 ENSG00000188039 NWD1

6 ENSG00000188229 TUBB4B

6 ENSG00000188316 ENO4

6 ENSG00000188352 FOCAD

6 ENSG00000188396 TCTEX1D4

6 ENSG00000188452 CERKL

6 ENSG00000188523 C9orf171

6 ENSG00000188596 C12orf55

6 ENSG00000188659 FAM154B

6 ENSG00000188817 SNTN

6 ENSG00000188921 PTPLAD2

6 ENSG00000188931 C1orf192

6 ENSG00000189157 FAM47E

6 ENSG00000196090 PTPRT

6 ENSG00000196169 KIF19

6 ENSG00000196230 TUBB

6 ENSG00000196236 XPNPEP3

6 ENSG00000196277 GRM7

6 ENSG00000196437 ZNF569

6 ENSG00000196476 C20orf96

6 ENSG00000196482 ESRRG

6 ENSG00000196535 MYO18A

6 ENSG00000196659 TTC30B

6 ENSG00000196693 ZNF33B

6 ENSG00000196704 AMZ2

6 ENSG00000196814 MVB12B

6 ENSG00000196872 KIAA1211L

6 ENSG00000196890 HIST3H2BB

6 ENSG00000197057 DTHD1

6 ENSG00000197122 SRC

6 ENSG00000197168 NEK5

6 ENSG00000197208 SLC22A4

6 ENSG00000197580 BCO2

6 ENSG00000197584 KCNMB2

6 ENSG00000197603 C5orf42

6 ENSG00000197653 DNAH10

6 ENSG00000197748 WDR96

6 ENSG00000197826 C4orf22

6 ENSG00000197889 MEIG1

6 ENSG00000197980 LEKR1

6 ENSG00000198003 CCDC151

6 ENSG00000198088 NUP62CL

6 ENSG00000198125 MB

6 ENSG00000198157 HMGN5

6 ENSG00000198182 ZNF607

6 ENSG00000198551 ZNF627

6 ENSG00000198553 KCNRG

6 ENSG00000198624 CCDC69

6 ENSG00000198668 CALM1

6 ENSG00000198718 FAM179B

6 ENSG00000198729 PPP1R14C

6 ENSG00000198815 FOXJ3

6 ENSG00000198825 INPP5F

6 ENSG00000198860 TSEN15

6 ENSG00000198894 CIPC

6 ENSG00000198919 DZIP3

6 ENSG00000198945 L3MBTL3

6 ENSG00000198947 DMD

6 ENSG00000198960 ARMCX6

6 ENSG00000203301

6 ENSG00000203372

6 ENSG00000203485 INF2

6 ENSG00000203499 FAM83H-AS1

6 ENSG00000203666 EFCAB2

6 ENSG00000203705 TATDN3

6 ENSG00000203734 ECT2L

6 ENSG00000203778 FAM229B

6 ENSG00000203797 DDO

6 ENSG00000203865 ATP1A1OS

6 ENSG00000203965 EFCAB7

6 ENSG00000203985 LDLRAD1

6 ENSG00000204052 LRRC73

6 ENSG00000204070 SYS1

6 ENSG00000204104 TRAF3IP1

6 ENSG00000204356 NELFE

6 ENSG00000204390 HSPA1L

6 ENSG00000204428 LY6G5C

6 ENSG00000204438 GPANK1

6 ENSG00000204566 C10orf115

6 ENSG00000204599 TRIM39

6 ENSG00000204666

6 ENSG00000204682 CASC10

6 ENSG00000204711 C9orf135

6 ENSG00000204815 TTC25

6 ENSG00000204852 TCTN1

6 ENSG00000204860 FAM201A

6 ENSG00000204950 LRRC10B

6 ENSG00000205084 TMEM231

6 ENSG00000205129 C4orf47

6 ENSG00000205231 TTLL10-AS1

6 ENSG00000205240 OR7E36P

6 ENSG00000205593 DENND6B

6 ENSG00000205730 ITPRIPL2

6 ENSG00000205758 CRYZL1

6 ENSG00000205808 PPAPDC2

6 ENSG00000205930 C21orf49

6 ENSG00000206053 HN1L

6 ENSG00000206199 ANKUB1

6 ENSG00000206567

6 ENSG00000213085 CCDC19

6 ENSG00000213123 TCTEX1D2

6 ENSG00000213297 ZNF625-ZNF20

6 ENSG00000213533 TMEM110

6 ENSG00000213753 CENPBD1P1

6 ENSG00000213904 LIPE-AS1

6 ENSG00000213937 CLDN9

6 ENSG00000214114 MYCBP

6 ENSG00000214174 AMZ2P1

6 ENSG00000214413 BBIP1

6 ENSG00000214447 FAM187A

6 ENSG00000214575 CPEB1

6 ENSG00000214706 IFRD2

6 ENSG00000215187 FAM166B

6 ENSG00000215217 C5orf49

6 ENSG00000215475 SIAH3

6 ENSG00000215845 TSTD1

6 ENSG00000219626 FAM228B

6 ENSG00000221821 C6orf226

6 ENSG00000221838 AP4M1

6 ENSG00000221995 TIAF1

6 ENSG00000222046 DCDC2B

6 ENSG00000223343

6 ENSG00000223547 ZNF844

6 ENSG00000223658

6 ENSG00000224038

6 ENSG00000224049

6 ENSG00000224165 DNAJC27-AS1

6 ENSG00000224281 SLC25A5-AS1

6 ENSG00000224479

6 ENSG00000224699 LAMTOR5-AS1

6 ENSG00000225302

6 ENSG00000225361 PPP1R26-AS1

6 ENSG00000225377

6 ENSG00000225431

6 ENSG00000225766

6 ENSG00000226026

6 ENSG00000226137 BAIAP2-AS1

6 ENSG00000226471

6 ENSG00000226644

6 ENSG00000226711 FAM66C

6 ENSG00000226754

6 ENSG00000227084

6 ENSG00000227308

6 ENSG00000227630 LINC01132

6 ENSG00000227695 DNMBP-AS1

6 ENSG00000227877 LINC00948

6 ENSG00000228084

6 ENSG00000228242

6 ENSG00000228723 SRGAP3-AS2

6 ENSG00000228858

6 ENSG00000228889 UBAC2-AS1

6 ENSG00000229124 VIM-AS1

6 ENSG00000229980 TOB1-AS1

6 ENSG00000230062 ANKRD66

6 ENSG00000230873 STMND1

6 ENSG00000230943

6 ENSG00000231023 LINC00326

6 ENSG00000231028 LINC00271

6 ENSG00000231043

6 ENSG00000231621

6 ENSG00000231738 TSPAN19

6 ENSG00000231980

6 ENSG00000232415

6 ENSG00000232453

6 ENSG00000232859 LYRM9

6 ENSG00000232862

6 ENSG00000233170

6 ENSG00000233382 NKAPP1

6 ENSG00000233730

6 ENSG00000233936

6 ENSG00000234465 PINLYP

6 ENSG00000234478

6 ENSG00000234684 SDCBP2-AS1

6 ENSG00000234911 TEX21P

6 ENSG00000235106 LINC00094

6 ENSG00000235142

6 ENSG00000235162 C12orf75

6 ENSG00000235453 TOPORS-AS1

6 ENSG00000235527

6 ENSG00000236914

6 ENSG00000237188

6 ENSG00000239467

6 ENSG00000240137

6 ENSG00000240204 SMKR1

6 ENSG00000240875 LINC00886

6 ENSG00000241935 HOGA1

6 ENSG00000241990

6 ENSG00000242808 SOX2-OT

6 ENSG00000242852 ZNF709

6 ENSG00000243069 ARHGEF26-AS1

6 ENSG00000243627

6 ENSG00000243660 ZNF487

6 ENSG00000243667 WDR92

6 ENSG00000243701 LINC00883

6 ENSG00000243710 WDR65

6 ENSG00000243836 WDR86-AS1

6 ENSG00000243910 TUBA4B

6 ENSG00000244968 LIFR-AS1

6 ENSG00000245025

6 ENSG00000245248 USP2-AS1

6 ENSG00000245317

6 ENSG00000245573 BDNF-AS

6 ENSG00000245694 CRNDE

6 ENSG00000245750

6 ENSG00000246016

6 ENSG00000246250

6 ENSG00000246308

6 ENSG00000246705 H2AFJ

6 ENSG00000247081

6 ENSG00000247271 ZBED5-AS1

6 ENSG00000247311

6 ENSG00000247363

6 ENSG00000247746 USP51

6 ENSG00000247796

6 ENSG00000247853

6 ENSG00000248008 DYNLL1-AS1

6 ENSG00000248508 SRP14-AS1

6 ENSG00000248712 CCDC153

6 ENSG00000248801

6 ENSG00000248905 FMN1

6 ENSG00000248932

6 ENSG00000249042

6 ENSG00000249241

6 ENSG00000249348 UGDH-AS1

6 ENSG00000249481 SPATS1

6 ENSG00000249610

6 ENSG00000249621

6 ENSG00000250056 LINC01018

6 ENSG00000250462 LRRC37BP1

6 ENSG00000250510 GPR162

6 ENSG00000250790

6 ENSG00000251307

6 ENSG00000251503 APITD1-CORT

6 ENSG00000251602

6 ENSG00000251669 FAM86EP

6 ENSG00000253302 STAU2-AS1

6 ENSG00000253320

6 ENSG00000253379

6 ENSG00000253719 ATXN7L3B

6 ENSG00000253948

6 ENSG00000254024

6 ENSG00000254389 RHPN1-AS1

6 ENSG00000254473

6 ENSG00000254608

6 ENSG00000254837

6 ENSG00000255036

6 ENSG00000255277 ABCC6P2

6 ENSG00000256061 DYX1C1

6 ENSG00000256073 C21orf119

6 ENSG00000257057 LINC01171

6 ENSG00000257084

6 ENSG00000257108 NHLRC4

6 ENSG00000257542 OR7E47P

6 ENSG00000257698

6 ENSG00000258334

6 ENSG00000258539

6 ENSG00000258701 LINC00638

6 ENSG00000258940

6 ENSG00000259087

6 ENSG00000259225

6 ENSG00000259251

6 ENSG00000259264

6 ENSG00000259319

6 ENSG00000259426

6 ENSG00000259577

6 ENSG00000259802

6 ENSG00000259901

6 ENSG00000260018

6 ENSG00000260057

6 ENSG00000260136

6 ENSG00000260328

6 ENSG00000260372 AQP4-AS1

6 ENSG00000260517

6 ENSG00000260526

6 ENSG00000260604

6 ENSG00000260643

6 ENSG00000260908

6 ENSG00000260951

6 ENSG00000261188

6 ENSG00000261572

6 ENSG00000261652 C15orf65

6 ENSG00000261759

6 ENSG00000261777

6 ENSG00000263011

6 ENSG00000263812 LINC00908

6 ENSG00000265666

6 ENSG00000265688 MAFG-AS1

6 ENSG00000265752

6 ENSG00000266947

6 ENSG00000267100 ILF3-AS1

6 ENSG00000267106 C19orf82

6 ENSG00000267128 RNF157-AS1

6 ENSG00000267348

6 ENSG00000267390

6 ENSG00000267439

6 ENSG00000267848

6 ENSG00000268061 NAPA-AS1

6 ENSG00000268175

6 ENSG00000268565

6 ENSG00000269916

6 ENSG00000270021

6 ENSG00000270362 HMGN3-AS1

6 ENSG00000270504

6 ENSG00000270820

6 ENSG00000271133

6 ENSG00000271853

6 ENSG00000272079

6 ENSG00000272086

6 ENSG00000272106

6 ENSG00000272143 FGF14-AS2

6 ENSG00000272168 CASC15

6 ENSG00000272288

6 ENSG00000272323

6 ENSG00000272442

6 ENSG00000272502

6 ENSG00000272514

6 ENSG00000272831

6 ENSG00000272902

6 ENSG00000273061

6 ENSG00000273071

7 ENSG00000008988 RPS20

7 ENSG00000063046 EIF4B

7 ENSG00000063177 RPL18

7 ENSG00000071082 RPL31

7 ENSG00000083845 RPS5

7 ENSG00000084090 STARD7

7 ENSG00000089009 RPL6

7 ENSG00000089157 RPLP0

7 ENSG00000089289 IGBP1

7 ENSG00000100129 EIF3L

7 ENSG00000100316 RPL3

7 ENSG00000100353 EIF3D

7 ENSG00000100814 CCNB1IP1

7 ENSG00000104408 EIF3E

7 ENSG00000104529 EEF1D

7 ENSG00000105193 RPS16

7 ENSG00000105202 FBL

7 ENSG00000105372 RPS19

7 ENSG00000105373 GLTSCR2

7 ENSG00000105640 RPL18A

7 ENSG00000107625 DDX50

7 ENSG00000108107 RPL28

7 ENSG00000108298 RPL19

7 ENSG00000108604 SMARCD2

7 ENSG00000109475 RPL34

7 ENSG00000110700 RPS13

7 ENSG00000111678 C12orf57

7 ENSG00000112306 RPS12

7 ENSG00000114391 RPL24

7 ENSG00000114942 EEF1B2

7 ENSG00000115268 RPS15

7 ENSG00000116251 RPL22

7 ENSG00000117543 DPH5

7 ENSG00000118181 RPS25

7 ENSG00000118816 CCNI

7 ENSG00000122026 RPL21

7 ENSG00000122406 RPL5

7 ENSG00000124614 RPS10

7 ENSG00000125691 RPL23

7 ENSG00000125743 SNRPD2

7 ENSG00000126088 UROD

7 ENSG00000129158 SERGEF

7 ENSG00000130159 ECSIT

7 ENSG00000130255 RPL36

7 ENSG00000130312 MRPL34

7 ENSG00000131143 COX4I1

7 ENSG00000131469 RPL27

7 ENSG00000133112 TPT1

7 ENSG00000134419 RPS15A

7 ENSG00000135390 ATP5G2

7 ENSG00000136104 RNASEH2B

7 ENSG00000136710 CCDC115

7 ENSG00000136942 RPL35

7 ENSG00000137054 POLR1E

7 ENSG00000137154 RPS6

7 ENSG00000137818 RPLP1

7 ENSG00000137970 RPL7P9

7 ENSG00000138326 RPS24

7 ENSG00000139239 RPL14P1

7 ENSG00000140905 GCSH

7 ENSG00000140988 RPS2

7 ENSG00000142534 RPS11

7 ENSG00000142541 RPL13A

7 ENSG00000142676 RPL11

7 ENSG00000142937 RPS8

7 ENSG00000143947 RPS27A

7 ENSG00000144713 RPL32

7 ENSG00000144741 SLC25A26

7 ENSG00000145425 RPS3A

7 ENSG00000145592 RPL37

7 ENSG00000145741 BTF3

7 ENSG00000147403 RPL10

7 ENSG00000147604 RPL7

7 ENSG00000147654 EBAG9

7 ENSG00000147677 EIF3H

7 ENSG00000148303 RPL7A

7 ENSG00000149273 RPS3

7 ENSG00000149806 FAU

7 ENSG00000151353 TMEM18

7 ENSG00000156482 RPL30

7 ENSG00000156508 EEF1A1

7 ENSG00000156853 ZNF689

7 ENSG00000161016 RPL8

7 ENSG00000161970 RPL26

7 ENSG00000162244 RPL29

7 ENSG00000163344 PMVK

7 ENSG00000163682 RPL9

7 ENSG00000164587 RPS14

7 ENSG00000166441 RPL27A

7 ENSG00000166902 MRPL16

7 ENSG00000167526 RPL13

7 ENSG00000168028 RPSA

7 ENSG00000169100 SLC25A6

7 ENSG00000169714 CNBP

7 ENSG00000170889 RPS9

7 ENSG00000171858 RPS21

7 ENSG00000171863 RPS7

7 ENSG00000172809 RPL38

7 ENSG00000173726 TOMM20

7 ENSG00000174444 RPL4

7 ENSG00000174547 MRPL11

7 ENSG00000174748 RPL15

7 ENSG00000175061 FAM211A-AS1

7 ENSG00000175390 EIF3F

7 ENSG00000177410 ZFAS1

7 ENSG00000177600 RPLP2

7 ENSG00000177954 RPS27

7 ENSG00000178464

7 ENSG00000182774 RPS17L

7 ENSG00000182899 RPL35A

7 ENSG00000183405 RPS7P1

7 ENSG00000184779 RPS17

7 ENSG00000185641

7 ENSG00000186468 RPS23

7 ENSG00000188243 COMMD6

7 ENSG00000188846 RPL14

7 ENSG00000189343 RPS2P46

7 ENSG00000196205 EEF1A1P5

7 ENSG00000196531 NACA

7 ENSG00000196683 TOMM7

7 ENSG00000197756 RPL37A

7 ENSG00000197958 RPL12

7 ENSG00000198034 RPS4X

7 ENSG00000198242 RPL23A

7 ENSG00000198546 ZNF511

7 ENSG00000198755 RPL10A

7 ENSG00000198918 RPL39

7 ENSG00000204196

7 ENSG00000204387 C6orf48

7 ENSG00000204628 GNB2L1

7 ENSG00000205246 RPSAP58

7 ENSG00000212802 RPL15P3

7 ENSG00000213178

7 ENSG00000213442 RPL18AP3

7 ENSG00000213553 RPLP0P6

7 ENSG00000213741 RPS29

7 ENSG00000213860 RPL21P75

7 ENSG00000214046 SMIM7

7 ENSG00000214113 LYRM4

7 ENSG00000214389 RPS3AP26

7 ENSG00000214485 RPL7P1

7 ENSG00000214784

7 ENSG00000215021 PHB2

7 ENSG00000218426

7 ENSG00000220749 RPL21P28

7 ENSG00000220842

7 ENSG00000221983 UBA52

7 ENSG00000226084

7 ENSG00000226221

7 ENSG00000227063 RPL41P1

7 ENSG00000227081

7 ENSG00000229117 RPL41

7 ENSG00000229638 RPL4P4

7 ENSG00000230629 RPS23P8

7 ENSG00000231500 RPS18

7 ENSG00000232472 EEF1B2P3

7 ENSG00000232573 RPL3P4

7 ENSG00000233476 EEF1A1P6

7 ENSG00000233762

7 ENSG00000233913

7 ENSG00000233927 RPS28

7 ENSG00000234741 GAS5

7 ENSG00000234797 RPS3AP6

7 ENSG00000234851

7 ENSG00000235065 RPL24P2

7 ENSG00000235552 RPL6P27

7 ENSG00000236552 RPL13AP5

7 ENSG00000240087

7 ENSG00000240342 RPS2P5

7 ENSG00000241343 RPL36A

7 ENSG00000242071 RPL7AP6

7 ENSG00000242299

7 ENSG00000243199

7 ENSG00000244313

7 ENSG00000244398

7 ENSG00000244716

7 ENSG00000245910 SNHG6

7 ENSG00000254772 EEF1G

7 ENSG00000265681 RPL17

7 ENSG00000269893 SNHG8

8 ENSG00000000938 FGR

8 ENSG00000005844 ITGAL

8 ENSG00000006074 CCL18

8 ENSG00000006075 CCL3

8 ENSG00000008516 MMP25

8 ENSG00000009790 TRAF3IP3

8 ENSG00000010295 IFFO1

8 ENSG00000010671 BTK

8 ENSG00000010810 FYN

8 ENSG00000011600 TYROBP

8 ENSG00000012779 ALOX5

8 ENSG00000013725 CD6

8 ENSG00000015285 WAS

8 ENSG00000018280 SLC11A1

8 ENSG00000019169 MARCH

8 ENSG00000023902 PLEKHO1

8 ENSG00000026297 RNASET2

8 ENSG00000027869 SH2D2A

8 ENSG00000028137 TNFRSF1B

8 ENSG00000033327 GAB2

8 ENSG00000038945 MSR1

8 ENSG00000043462 LCP2

8 ENSG00000048740 CELF2

8 ENSG00000054967 RELT

8 ENSG00000057657 PRDM1

8 ENSG00000059377 TBXAS1

8 ENSG00000059728 MXD1

8 ENSG00000059804 SLC2A3

8 ENSG00000062282 DGAT2

8 ENSG00000064201 TSPAN32

8 ENSG00000065413 ANKRD44

8 ENSG00000065675 PRKCQ

8 ENSG00000066294 CD84

8 ENSG00000066336 SPI1

8 ENSG00000068831 RASGRP2

8 ENSG00000069424 KCNAB2

8 ENSG00000072401 UBE2D1

8 ENSG00000072694 FCGR2B

8 ENSG00000072786 STK10

8 ENSG00000072818 ACAP1

8 ENSG00000073921 PICALM

8 ENSG00000074706 IPCEF1

8 ENSG00000074966 TXK

8 ENSG00000075624 ACTB

8 ENSG00000075884 ARHGAP15

8 ENSG00000076641 PAGE1

8 ENSG00000076662 ICAM3

8 ENSG00000076928 ARHGEF1

8 ENSG00000077420 APBB1IP

8 ENSG00000077984 CST7

8 ENSG00000078589 P2RY10

8 ENSG00000079263 SP140

8 ENSG00000081059 TCF7

8 ENSG00000081087 OSTM1

8 ENSG00000081237 PTPRC

8 ENSG00000081320 STK17B

8 ENSG00000082074 FYB

8 ENSG00000085265 FCN1

8 ENSG00000085514 CHILD

8 ENSG00000086300 SNX10

8 ENSG00000086730 LAT2

8 ENSG00000087266 SH3BP2

8 ENSG00000088827 SIGLEC1

8 ENSG00000089327 FXYD5

8 ENSG00000089639 GMIP

8 ENSG00000089820 ARHGAP4

8 ENSG00000090339 ICAM1

8 ENSG00000090674 MCOLN1

8 ENSG00000091106 NLRC4

8 ENSG00000092929 UNC13D

8 ENSG00000095303 PTGS1

8 ENSG00000095370 SH2D3C

8 ENSG00000096996 IL12RB1

8 ENSG00000099308 MAST3

8 ENSG00000099985 OSM

8 ENSG00000100055 CYTH4

8 ENSG00000100060 MFNG

8 ENSG00000100351 GRAP2

8 ENSG00000100365 NCF4

8 ENSG00000100368 CSF2RB

8 ENSG00000100385 IL2RB

8 ENSG00000100599 RIN3

8 ENSG00000100985 MMP9

8 ENSG00000101109 STK4

8 ENSG00000101265 RASSF2

8 ENSG00000101307 SIRPB1

8 ENSG00000101336 HCK

8 ENSG00000101916 TLR8

8 ENSG00000102032 RENBP

8 ENSG00000102218 RP2

8 ENSG00000102445 KIAA0226L

8 ENSG00000102524 TNFSF13B

8 ENSG00000102575 ACP5

8 ENSG00000102879 CORO1A

8 ENSG00000103005 USB1

8 ENSG00000103187 COTL1

8 ENSG00000103313 MEFV

8 ENSG00000103522 IL21R

8 ENSG00000103569 AQP9

8 ENSG00000104814 MAP4K1

8 ENSG00000104894 CD37

8 ENSG00000104972 LILRB1

8 ENSG00000104998 IL27RA

8 ENSG00000105122 RASAL3

8 ENSG00000105329 TGFB1

8 ENSG00000105339 DENND3

8 ENSG00000105483 CARD8

8 ENSG00000105639 JAK3

8 ENSG00000105835 NAMPT

8 ENSG00000105851 PIK3CG

8 ENSG00000105967 TFEC

8 ENSG00000106066 CPVL

8 ENSG00000106348 IMPDH1

8 ENSG00000107099 DOCK8

8 ENSG00000107485 GATA3

8 ENSG00000107551 RASSF4

8 ENSG00000108405 P2RX1

8 ENSG00000108932 SLC16A6

8 ENSG00000108960 MMD

8 ENSG00000109743 BST1

8 ENSG00000110031 LPXN

8 ENSG00000110047 EHD1

8 ENSG00000110077 MS4A6A

8 ENSG00000110079 MS4A4A

8 ENSG00000110324 IL10RA

8 ENSG00000110395 CBL

8 ENSG00000110446 SLC15A3

8 ENSG00000110448 CD5

8 ENSG00000110848 CD69

8 ENSG00000110876 SELPLG

8 ENSG00000110934 BIN2

8 ENSG00000111252 SH2B3

8 ENSG00000111348 ARHGDIB

8 ENSG00000111679 PTPN6

8 ENSG00000111729 CLEC4A

8 ENSG00000112096 SOD2

8 ENSG00000112137 PACTR1

8 ENSG00000112149 CD83

8 ENSG00000112195 TREML2

8 ENSG00000112303 VNN2

8 ENSG00000112531 QKI

8 ENSG00000112799 LY86

8 ENSG00000113263 ITK

8 ENSG00000113273 ARSB

8 ENSG00000114013 CD86

8 ENSG00000114450 GNB4

8 ENSG00000114626 ABTB1

8 ENSG00000114737 CISH

8 ENSG00000115085 ZAP70

8 ENSG00000115165 CYTIP

8 ENSG00000115232 ITGA4

8 ENSG00000115271 GCA

8 ENSG00000115318 LOXL3

8 ENSG00000115325 DOK1

8 ENSG00000115355 CCDC88A

8 ENSG00000115604 IL18R1

8 ENSG00000115607 IL18RAP

8 ENSG00000115756 HPCAL1

8 ENSG00000115828 QPCT

8 ENSG00000115935 WIPF1

8 ENSG00000115956 PLEK

8 ENSG00000116017 ARID3A

8 ENSG00000116337 AMPD2

8 ENSG00000116701 NCF2

8 ENSG00000116741 RGS2

8 ENSG00000116824 CD2

8 ENSG00000116852 KIF21B

8 ENSG00000117009 KMO

8 ENSG00000117090 SLAMF1

8 ENSG00000117091 CD48

8 ENSG00000117115 PADI2

8 ENSG00000117281 CD160

8 ENSG00000118263 KLF7

8 ENSG00000118508 RAB32

8 ENSG00000119321 FKBP15

8 ENSG00000119535 CSF3R

8 ENSG00000119686 FLVCR2

8 ENSG00000120063 GNA13

8 ENSG00000120709 FAM53C

8 ENSG00000120899 PTK2B

8 ENSG00000121060 TRIM25

8 ENSG00000121210 KIAA0922

8 ENSG00000121281 ADCY7

8 ENSG00000121797 CCRL2

8 ENSG00000121807 CCR2

8 ENSG00000121966 CXCR4

8 ENSG00000122122 SASH3

8 ENSG00000122188 LAX1

8 ENSG00000122224 LY9

8 ENSG00000122862 SRGN

8 ENSG00000122986 HVCN1

8 ENSG00000123329 ARHGAP9

8 ENSG00000123338 NCKAP1L

8 ENSG00000123689 G0S2

8 ENSG00000124126 PREX1

8 ENSG00000124203 ZNF831

8 ENSG00000124334 IL9R

8 ENSG00000124357 NAGK

8 ENSG00000124491 F13A1

8 ENSG00000124731 TRAIN1

8 ENSG00000125354 6-Sep

8 ENSG00000125538 IL1B

8 ENSG00000125637 PSD4

8 ENSG00000125735 TNFSF14

8 ENSG00000125910 S1PR4

8 ENSG00000126246 IGFLR1

8 ENSG00000126262 FFAR2

8 ENSG00000126264 HCST

8 ENSG00000126353 CCR7

8 ENSG00000126561 STAT5A

8 ENSG00000126860 EVI2A

8 ENSG00000126882 FAM78A

8 ENSG00000127084 FGD3

8 ENSG00000127152 BCL11B

8 ENSG00000127507 EMR2

8 ENSG00000127951 FGL2

8 ENSG00000128271 ADORA2A

8 ENSG00000128340 RAC2

8 ENSG00000128383 APOBEC3A

8 ENSG00000128815 WDFY4

8 ENSG00000129071 MBD4

8 ENSG00000129226 CD68

8 ENSG00000129277 CCL4

8 ENSG00000129657 SEC14L1

8 ENSG00000129675 ARHGEF6

8 ENSG00000130203 APOE

8 ENSG00000130208 APOC1

8 ENSG00000130429 ARPC1B

8 ENSG00000130475 FCHO1

8 ENSG00000130592 LSP1

8 ENSG00000130755 GMFG

8 ENSG00000130775 THEMIS2

8 ENSG00000130830 MPP1

8 ENSG00000131042 LILRB2

8 ENSG00000131378 RFTN1

8 ENSG00000131401 NAPSB

8 ENSG00000131669 NINJ1

8 ENSG00000131724 IL13RA1

8 ENSG00000132182 NUP210

8 ENSG00000132205 EMILIN2

8 ENSG00000132334 PTPRE

8 ENSG00000132510 KDM6B

8 ENSG00000132514 CLEC10A

8 ENSG00000132965 ALOX5AP

8 ENSG00000133048 CHI3L1

8 ENSG00000133246 PRAM1

8 ENSG00000133574 GIMAP4

8 ENSG00000133961 NUMB

8 ENSG00000134242 PTPN22

8 ENSG00000134516 DOCK2

8 ENSG00000134668 SPOCD1

8 ENSG00000134686 PHC2

8 ENSG00000134698 AUG4

8 ENSG00000134830 C5AR2

8 ENSG00000134954 ETS1

8 ENSG00000135074 ADAM19

8 ENSG00000135077 HAVCR2

8 ENSG00000135218 CD36

8 ENSG00000135426 TESPA1

8 ENSG00000135439 AGAP2

8 ENSG00000135604 STX11

8 ENSG00000135636 DYSF

8 ENSG00000135838 NPL

8 ENSG00000135905 DOCK10

8 ENSG00000136040 PLXNC1

8 ENSG00000136111 TBC1D4

8 ENSG00000136167 LCP1

8 ENSG00000136250 AOAH

8 ENSG00000136286 MYO1G

8 ENSG00000136404 TM6SF1

8 ENSG00000136490 LIMD2

8 ENSG00000136560 TANK

8 ENSG00000136867 SLC31A2

8 ENSG00000136869 TLR4

8 ENSG00000137076 TLN1

8 ENSG00000137078 SIT1

8 ENSG00000137265 IRF4

8 ENSG00000137462 TLR2

8 ENSG00000137491 SLCO2B1

8 ENSG00000137575 SDCBP

8 ENSG00000137752 CASP1

8 ENSG00000137841 PLCB2

8 ENSG00000138378 STAT4

8 ENSG00000138621 PPCDC

8 ENSG00000138964 PARVG

8 ENSG00000139193 CD27

8 ENSG00000139278 GLIPR1

8 ENSG00000139370 SLC15A4

8 ENSG00000139436 GIT2

8 ENSG00000140030 GPR65

8 ENSG00000140368 PSTPIP1

8 ENSG00000140379 BCL2A1

8 ENSG00000140678 ITGAX

8 ENSG00000140749 IGSF6

8 ENSG00000140931 CMTM3

8 ENSG00000140968 IRF8

8 ENSG00000141293 SKAP1

8 ENSG00000141298 SSH2

8 ENSG00000141480 ARRB2

8 ENSG00000141506 PIK3R5

8 ENSG00000141576 RNF157

8 ENSG00000142185 TRPM2

8 ENSG00000142227 EMP3

8 ENSG00000142347 MYO1F

8 ENSG00000142512 SIGLEC10

8 ENSG00000143110 C1orf162

8 ENSG00000143119 CD53

8 ENSG00000143226 FCGR2A

8 ENSG00000143382 ADAMTSL4

8 ENSG00000143546 S100A8

8 ENSG00000143851 PTPN7

8 ENSG00000144218 AFF3

8 ENSG00000144815 NXPE3

8 ENSG00000145416 1-Mar

8 ENSG00000145569 FAM105A

8 ENSG00000145649 GZMA

8 ENSG00000145819 ARHGAP26

8 ENSG00000146070 PLA2G7

8 ENSG00000146094 DOK3

8 ENSG00000146112 PPP1R18

8 ENSG00000146192 FGD2

8 ENSG00000146278 PNRC1

8 ENSG00000146285 SCML4

8 ENSG00000146592 CREB5

8 ENSG00000146859 TMEM140

8 ENSG00000147010 SH3KBP1

8 ENSG00000147065 MSN

8 ENSG00000147168 IL2RG

8 ENSG00000147251 DOCK11

8 ENSG00000147416 ATP6V1B2

8 ENSG00000147443 DOK2

8 ENSG00000147454 SLC25A37

8 ENSG00000147459 DOCK5

8 ENSG00000147872 PLIN2

8 ENSG00000148572 NRBF2

8 ENSG00000148908 RGS10

8 ENSG00000149091 DGKZ

8 ENSG00000149177 PTPRJ

8 ENSG00000149781 FERMT3

8 ENSG00000150337 FCGR1A

8 ENSG00000150681 RGS18

8 ENSG00000150867 PIP4K2A

8 ENSG00000151490 PTPRO

8 ENSG00000151651 ADAM8

8 ENSG00000151702 FLI1

8 ENSG00000151726 ACSL1

8 ENSG00000151948 GLT1D1

8 ENSG00000152213 ARL11

8 ENSG00000152270 PDE3B

8 ENSG00000152495 CAMK4

8 ENSG00000153071 DAB2

8 ENSG00000153179 RASSF3

8 ENSG00000153283 CD96

8 ENSG00000153317 ASAP1

8 ENSG00000153395 LPCAT1

8 ENSG00000153563 CD8A

8 ENSG00000154016 GRAP

8 ENSG00000154451 GBP5

8 ENSG00000154589 LY96

8 ENSG00000155307 SAMSN1

8 ENSG00000155465 SLC7A7

8 ENSG00000155629 PIK3AP1

8 ENSG00000155659 VSIG4

8 ENSG00000155849 ELMO1

8 ENSG00000155926 SLA

8 ENSG00000156273 BACH1

8 ENSG00000157350 ST3GAL2

8 ENSG00000157551 KCNJ15

8 ENSG00000158517 NCF1

8 ENSG00000158714 SLAMF8

8 ENSG00000158869 FCER1G

8 ENSG00000159189 C1QC

8 ENSG00000159322 ADPGK

8 ENSG00000159618 GPR114

8 ENSG00000159753 RLTPR

8 ENSG00000160185 UBASH3A

8 ENSG00000160219 GAB3

8 ENSG00000160255 ITGB2

8 ENSG00000160326 SLC2A6

8 ENSG00000160593 AMICA1

8 ENSG00000160654 CD3G

8 ENSG00000160883 HK3

8 ENSG00000160999 SH2B2

8 ENSG00000161570 CCL5

8 ENSG00000161791 FMNL3

8 ENSG00000161929 SCIMP

8 ENSG00000162511 LAPTM5

8 ENSG00000162676 GFI1

8 ENSG00000162711 NLRP3

8 ENSG00000162739 SLAMF6

8 ENSG00000163154 TNFAIP8L2

8 ENSG00000163162 RNF149

8 ENSG00000163219 ARHGAP25

8 ENSG00000163220 S100A9

8 ENSG00000163376 KBTBD8

8 ENSG00000163421 PROK2

8 ENSG00000163464 CXCR1

8 ENSG00000163519 TRAT1

8 ENSG00000163563 MNDA

8 ENSG00000163564 PYHIN1

8 ENSG00000163600 ICOS

8 ENSG00000163823 CCR1

8 ENSG00000164691 TAGAP

8 ENSG00000165030 NFIL3

8 ENSG00000165168 CYBB

8 ENSG00000165178 NCF1C

8 ENSG00000166128 RAB8B

8 ENSG00000166340 TPP1

8 ENSG00000166501 PRKCB

8 ENSG00000166523 CLEC4E

8 ENSG00000166716 ZNF592

8 ENSG00000166927 MS4A7

8 ENSG00000167208 SNX20

8 ENSG00000167261 DPEP2

8 ENSG00000167286 CD3D

8 ENSG00000167483 FAM129C

8 ENSG00000167613 LAIR1

8 ENSG00000167680 SEMA6B

8 ENSG00000167851 CD300A

8 ENSG00000168067 MAP4K2

8 ENSG00000168071 CCDC88B

8 ENSG00000168404 MLKL

8 ENSG00000168421 RHOH

8 ENSG00000168685 IL7R

8 ENSG00000168918 INPP5D

8 ENSG00000169180 XPO6

8 ENSG00000169220 RGS14

8 ENSG00000169228 RAB24

8 ENSG00000169403 PTAFR

8 ENSG00000169413 RNASE6

8 ENSG00000169442 CD52

8 ENSG00000169508 GPR183

8 ENSG00000169554 ZEB2

8 ENSG00000169826 CSGALNACT2

8 ENSG00000169896 ITGAM

8 ENSG00000170323 FABP4

8 ENSG00000170458 CD14

8 ENSG00000170525 PFKFB3

8 ENSG00000170542 SERPINB9

8 ENSG00000170909 OSCAR

8 ENSG00000170956 CEACAM3

8 ENSG00000171049 FPR2

8 ENSG00000171051 FPR1

8 ENSG00000171488 LRRC8C

8 ENSG00000171608 PIK3CD

8 ENSG00000171659 GPR34

8 ENSG00000171700 RGS19

8 ENSG00000171777 RASGRP4

8 ENSG00000171860 C3AR1

8 ENSG00000172081 MOB3A

8 ENSG00000172116 CD8B

8 ENSG00000172216 CEBPB

8 ENSG00000172243 CLEC7A

8 ENSG00000172322 CLEC12A

8 ENSG00000172349 IL16

8 ENSG00000172543 CTSW

8 ENSG00000172575 RASGRP1

8 ENSG00000172673 THEMIS

8 ENSG00000173020 ADRBK1

8 ENSG00000173110 HSPA6

8 ENSG00000173200 PARP15

8 ENSG00000173281 PPP1R3B

8 ENSG00000173369 C1QB

8 ENSG00000173372 C1QA

8 ENSG00000173391 OLR1

8 ENSG00000173535 TNFRSF10C

8 ENSG00000173559 NABP1

8 ENSG00000173638 SLC19A1

8 ENSG00000173757 STAT5B

8 ENSG00000173762 CD7

8 ENSG00000173868 PHOSPHO1

8 ENSG00000174004 NRROS

8 ENSG00000174125 TLR1

8 ENSG00000174579 MSL2

8 ENSG00000174600 CMKLR1

8 ENSG00000174718 KIAA1551

8 ENSG00000175463 TBC1D10C

8 ENSG00000175489 LRRC25

8 ENSG00000175857 GAPT

8 ENSG00000176390 CRLF3

8 ENSG00000177105 RHOG

8 ENSG00000177575 CD163

8 ENSG00000177663 IL17RA

8 ENSG00000177885 GRB2

8 ENSG00000178562 CD28

8 ENSG00000178607 ERN1

8 ENSG00000179361 ARID3B

8 ENSG00000180096 1-Sep

8 ENSG00000180353 HCLS1

8 ENSG00000180448 HMHA1

8 ENSG00000180871 CXCR2

8 ENSG00000180953 ST20

8 ENSG00000181381 DDX60L

8 ENSG00000181409 AATK

8 ENSG00000181631 P2RY13

8 ENSG00000182022 CHST15

8 ENSG00000182287 AP1S2

8 ENSG00000182487 NCF1B

8 ENSG00000182511 FES

8 ENSG00000182578 CSF1R

8 ENSG00000182866 LCK

8 ENSG00000182885 GPR97

8 ENSG00000183019 C19orf59

8 ENSG00000183023 SLC8A1

8 ENSG00000183484 GPR132

8 ENSG00000183688 FAM101B

8 ENSG00000183748

8 ENSG00000183918 SH2D1A

8 ENSG00000184014 DENND5A

8 ENSG00000184060 ADAP2

8 ENSG00000184371 CSF1

8 ENSG00000184588 PDE4B

8 ENSG00000184602 SNN

8 ENSG00000184730 APOBR

8 ENSG00000184922 FMNL1

8 ENSG00000185201 IFITM2

8 ENSG00000185215 TNFAIP2

8 ENSG00000185339 TCN2

8 ENSG00000185477 GPRIN3

8 ENSG00000185811 IKZF1

8 ENSG00000185862 EVI2B

8 ENSG00000185947 ZNF267

8 ENSG00000186074 CD300LF

8 ENSG00000186469 GNG2

8 ENSG00000186517 ARHGAP30

8 ENSG00000186635 ARAP1

8 ENSG00000186818 LILRB4

8 ENSG00000187116 LILRA5

8 ENSG00000187239 FNBP1

8 ENSG00000187474 FPR3

8 ENSG00000187688 TRPV2

8 ENSG00000187764 SEMA4D

8 ENSG00000187796 CARD9

8 ENSG00000187994 RINL

8 ENSG00000188404 SELL

8 ENSG00000188820 FAM26F

8 ENSG00000188895 MSL1

8 ENSG00000188906 LRRK2

8 ENSG00000189067 LITAF

8 ENSG00000196511 TPK1

8 ENSG00000196549 MME

8 ENSG00000196663 TECPR2

8 ENSG00000196843 ARID5A

8 ENSG00000196954 CASP4

8 ENSG00000197081 IGF2R

8 ENSG00000197249 SERPINA1

8 ENSG00000197471 SPN

8 ENSG00000197629 MPEG1

8 ENSG00000197860 SGTB

8 ENSG00000197872 FAM49A

8 ENSG00000198053 SIRPA

8 ENSG00000198223 CSF2RA

8 ENSG00000198286 CARD11

8 ENSG00000198771 RCSD1

8 ENSG00000198821 CD247

8 ENSG00000198837 DENND4B

8 ENSG00000198846 TOX

8 ENSG00000198851 CD3E

8 ENSG00000198879 SFMBT2

8 ENSG00000203747 FCGR3A

8 ENSG00000204136 GGTA1P

8 ENSG00000204160 ZDHHC18

8 ENSG00000204267 TAP2

8 ENSG00000204397 CARD16

8 ENSG00000204472 AIF1

8 ENSG00000204482 LST1

8 ENSG00000204516 MICB

8 ENSG00000204577 LILRB3

8 ENSG00000204947 ZNF425

8 ENSG00000205269 TMEM170B

8 ENSG00000205744 DENND1C

8 ENSG00000211689 TRGC1

8 ENSG00000213203 GIMAP1

8 ENSG00000213402 PTPRCAP

8 ENSG00000213445 SIPA1

8 ENSG00000213654 GPSM3

8 ENSG00000213658 LAT

8 ENSG00000213809 KLRK1

8 ENSG00000215114 UBXN2B

8 ENSG00000216490 IFI30

8 ENSG00000217128 FNIP1

8 ENSG00000217555 CKLF

8 ENSG00000224397

8 ENSG00000227191 TRGC2

8 ENSG00000227507 LTB

8 ENSG00000229164 TRAC

8 ENSG00000229644 NAMPTL

8 ENSG00000235568 NFAM1

8 ENSG00000239998 LILRA2

8 ENSG00000241839 PLEKHO2

8 ENSG00000241878 PISD

8 ENSG00000242539

8 ENSG00000244482 LILRA6

8 ENSG00000247774 PCED1B-AS1

8 ENSG00000250264

8 ENSG00000255398 HCAR3

8 ENSG00000256007 ARAP1-AS1

8 ENSG00000258227 CLEC5A

8 ENSG00000265206 MIR142

8 ENSG00000267121

8 ENSG00000268001

8 ENSG00000269215

8 ENSG00000269728

9 ENSG00000002549 LAP3

9 ENSG00000013374 NUB1

9 ENSG00000019582 CD74

9 ENSG00000026950 BTN3A1

9 ENSG00000055332 EIF2AK2

9 ENSG00000059378 PARP12

9 ENSG00000067066 SP100

9 ENSG00000068079 IFI35

9 ENSG00000089692 LAG3

9 ENSG00000092010 PSME1

9 ENSG00000100336 APOL4

9 ENSG00000100342 APOL1

9 ENSG00000100911 PSME2

9 ENSG00000106785 TRIM14

9 ENSG00000107201 DDX58

9 ENSG00000111331 OAS3

9 ENSG00000111335 OAS2

9 ENSG00000111801 BTN3A3

9 ENSG00000112763 BTN2A1

9 ENSG00000114127 XRN1

9 ENSG00000115267 IFIH1

9 ENSG00000115415 STAT1

9 ENSG00000117228 GBP1

9 ENSG00000119917 IFIT3

9 ENSG00000121858 TNFSF10

9 ENSG00000123240 OPTN

9 ENSG00000123609 NMI

9 ENSG00000124201 ZNFX1

9 ENSG00000124226 RNF114

9 ENSG00000124508 BTN2A2

9 ENSG00000125347 IRF1

9 ENSG00000126709 IFI6

9 ENSG00000128284 APOL3

9 ENSG00000128335 APOL2

9 ENSG00000130303 BST2

9 ENSG00000130487 KLHDC7B

9 ENSG00000130589 HELZ2

9 ENSG00000131203 IDO1

9 ENSG00000132109 TRIM21

9 ENSG00000132274 TRIM22

9 ENSG00000133106 EPSTI1

9 ENSG00000134326 CMPK2

9 ENSG00000135148 TRAFD1

9 ENSG00000136816 TOR1B

9 ENSG00000137628 DDX60

9 ENSG00000137959 IFI44L

9 ENSG00000137965 IFI44

9 ENSG00000138496 PARP9

9 ENSG00000138642 HERC6

9 ENSG00000138755 CXCL9

9 ENSG00000140105 WARS

9 ENSG00000140464 PML

9 ENSG00000140853 NLRC5

9 ENSG00000152778 IFIT5

9 ENSG00000156587 UBE2L6

9 ENSG00000157601 MX1

9 ENSG00000158773 USF1

9 ENSG00000160710 ADAR

9 ENSG00000160932 LY6E

9 ENSG00000162654 GBP4

9 ENSG00000163840 DTX3L

9 ENSG00000164136 IL15

9 ENSG00000165949 IFI27

9 ENSG00000166278 C2

9 ENSG00000166710 B2M

9 ENSG00000168062 BATF2

9 ENSG00000168394 TAP1

9 ENSG00000168961 LGALS9

9 ENSG00000169245 CXCL10

9 ENSG00000173193 PARP14

9 ENSG00000173821 RNF213

9 ENSG00000177409 SAMD9L

9 ENSG00000179344 HLA-DQB1

9 ENSG00000179583 CIITA

9 ENSG00000185338 SOCS1

9 ENSG00000185404 SP140L

9 ENSG00000185880 TRIM69

9 ENSG00000186470 BTN3A2

9 ENSG00000187608 ISG15

9 ENSG00000188282 RUFY4

9 ENSG00000188313 PLSCR1

9 ENSG00000196126 HLA-DRB1

9 ENSG00000196735 HLA-DQA1

9 ENSG00000197142 ACSL5

9 ENSG00000197536 C5orf56

9 ENSG00000204252 HLA-DOA

9 ENSG00000204257 HLA-DMA

9 ENSG00000204261 TAPSAR1

9 ENSG00000204264 PSMB8

9 ENSG00000204287 HLA-DRA

9 ENSG00000204525 HLA-C

9 ENSG00000204592 HLA-E

9 ENSG00000204642 HLA-F

9 ENSG00000205220 PSMB10

9 ENSG00000205436 EXOC3L4

9 ENSG00000206337 HCP5

9 ENSG00000206503 HLA-A

9 ENSG00000213886 UBD

9 ENSG00000213928 IRF9

9 ENSG00000221963 APOL6

9 ENSG00000223865 HLA-DPB1

9 ENSG00000225131 PSME2P2

9 ENSG00000225492 GBP1P1

9 ENSG00000231389 HLA-DPA1

9 ENSG00000231925 TAPBP

9 ENSG00000232629 HLA-DQB2

9 ENSG00000234745 HLA-B

9 ENSG00000237988 OR2I1P

9 ENSG00000240065 PSMB9

9 ENSG00000242574 HLA-DMB

9 ENSG00000263013

9 ENSG00000269640

10 ENSG00000167535 CACNB3

10 ENSG00000109339 MAPK10

Table 14. 22 genes that were selected from

3,936 to predict the molecular subtypes in the validation cohort (endobronchial biopsy) Gene Module Gene Name EnsemblID 1 PHLDB1 ENSG00000019144 1 MARVELD1 ENSG00000155254 1 KIRREL1 ENSG00000183853 2 CCNL2 ENSG00000221978 2 MSANTD2 ENSG00000120458 2 LUC7L ENSG00000007392 3 BTG2 ENSG00000159388 3 ZFP36 ENSG00000128016 4 COX6A1 ENSG00000111775 4 COX7A2 ENSG00000112695 5 RACGAP1 ENSG00000161800 5 TPX2 ENSG00000088325 6 NEK11 ENSG00000114670 6 IFT88 ENSG00000032742 7 RPL26 ENSG00000161970 7 RPL23 ENSG00000125691 8 DOCK2 ENSG00000134516 8 CD53 ENSG00000143119 8 LAPTM1625 ENSG00000

9 UBE2L6 ENSG00000156587 9 EPSTI1 ENSG00000133106 9 TAP1 ENSG00000168394 Table 15. 8 genes that were selected from the 22 genes (Table 14) to predict the Proliferative or not Proliferative subtype in bronchial smears Gene Module Gene Name EnsemblID 4 COX6A1 ENSG00000111775 COX6A1 ENSG00000111775 ENSG00000161800 5 TPX2 ENSG00000088325 6 NEK11 ENSG00000114670 6 IFT88 ENSG00000032742 7 RPL26 ENSG00000161970 7 RPL23 ENSG00000125691 Table 16. 112 genes used to predict progression/persistence versus regression in endobronchial biopsies classified as being in the Proliferative subtype. Genes in Module 9 associated with progression/regression. These genes are contained in Table

13.

EnsemblID Gene Symbols

ENSG00000002549 LAP3

ENSG00000013374 NUB1

ENSG00000019582 CD74

ENSG00000026950 BTN3A1

ENSG00000055332 EIF2AK2

ENSG00000059378 PARP12

ENSG00000067066 SP100

ENSG00000068079 IFI35

ENSG00000089692 LAG3

ENSG00000092010 PSME1

ENSG00000100336 APOL4

ENSG00000100342 APOL1

ENSG00000100911 PSME2

ENSG00000106785 TRIM14

ENSG00000107201 DDX58

ENSG00000111331 OAS3

ENSG00000111335 OAS2

ENSG00000111801 BTN3A3

ENSG00000112763 BTN2A1

ENSG00000114127 XRN1

ENSG00000115267 IFIH1

ENSG00000115415 STAT1

ENSG00000117228 GBP1

ENSG00000119917 IFIT3

ENSG000001121858 TNFSF10

ENSG00000123240 OPTN

ENSG00000123609 NMI

ENSG00000124201 ZNFX1

ENSG00000124226 RNF114

ENSG00000124508 BTN2A2

ENSG00000125347 IRF1

ENSG00000126709 IFI6

ENSG00000128284 APOL3

ENSG00000128335 APOL2

ENSG00000130303 BST2

ENSG00000130487 KLHDC7B

ENSG00000130589 HELZ2

ENSG00000131203 IDO1

ENSG00000132109 TRIM21

ENSG00000132274 TRIM22

ENSG00000133106 EPSTI1

ENSG00000134326 CMPK2

ENSG00000135148 TRAFD1

ENSG00000136816 TOR1B

ENSG00000137628 DDX60

ENSG00000137959 IFI44L

ENSG00000137965 IFI44

ENSG00000138496 PARP9

ENSG00000138642 HERC6

ENSG00000138755 CXCL9

ENSG00000140105 WARS

ENSG00000140464 PML

ENSG00000140853 NLRC5

ENSG00000152778 IFIT5

ENSG00000156587 UBE2L6

ENSG00000157601 MX1

ENSG00000158773 USF1

ENSG00000160710 ADAR

ENSG00000160932 LY6E

ENSG00000162654 GBP4

ENSG00000163840 DTX3L

ENSG00000164136 IL15

ENSG00000165949 IFI27

ENSG00000166278 C2

ENSG00000166710 B2M

ENSG00000168062 BATF2

ENSG00000168394 TAP1

ENSG00000168961 LGALS9

ENSG00000169245 CXCL10

ENSG00000173193 PARP14

ENSG00000173821 RNF213

ENSG00000177409 SAMD9L

ENSG00000179344 HLA-DQB1

ENSG00000179583 CIITA

ENSG00000185338 SOCS1

ENSG00000185404 SP140L

ENSG00000185880 TRIM69

ENSG00000186470 BTN3A2

ENSG00000187608 ISG15

ENSG00000188282 RUFY4

ENSG00000188313 PLSCR1

ENSG00000196126 HLA-DRB1

ENSG00000196735 HLA-DQA1

ENSG00000197142 ACSL5

ENSG00000197536 C5orf56

ENSG00000204252 HLA-DOA

ENSG00000204257 HLA-DMA

ENSG00000204261 TAPSAR1

ENSG00000204264 PSMB8

ENSG00000204287 HLA-DRA

ENSG00000204525 HLA-C

ENSG00000204592 HLA-E

ENSG00000204642 HLA-F

ENSG00000205220 PSMB10

ENSG00000205436 EXOC3L4

ENSG00000206337 HCP5

ENSG00000206503 HLA-A

ENSG00000213886 UBD

ENSG00000213928 IRF9

ENSG00000221963 APOL6

ENSG00000223865 HLA-DPB1

ENSG00000225131 PSME2P2

ENSG00000225492 GBP1P1

ENSG00000231389 HLA-DPA1

ENSG00000231925 TAPBP

ENSG00000232629 HLA-DQB2

ENSG00000234745 HLA-B

ENSG00000237988 OR2I1P

ENSG00000240065 PSMB9

ENSG00000242574 HLA-DMB

ENSG00000263013 RP11-876N24.5

ENSG00000269640

[0175] The methods described in this document refer to the determination of the expression level of at least one gene. In some embodiments of either aspect, at least one of the gene may be one or more genes selected from Tables 13, 14, 15, and/or 16. In some embodiments of either aspect, the Tables gene lists 13, 14, and 16 are relevant for endobronchial biopsy specimens that range in histology from normal to premalignant. In some modalities of either aspect, where the sample is an endobronchial biopsy specimen, one or more genes are selected from Table 13, 14, and/or 16. In some modalities of either aspect, Table 15 is relevant to normal bronchial smears. In some modalities of either aspect, where the sample is a bronchial smear sample (eg, normal tissue), one or more genes are selected from Table 15.

[0176] In some embodiments of either aspect, one or more genes selected from Table 13 or 16 are not B2M, HLA-DRA, HLA-DRB1 or HLA-DPA1. In some embodiments of either aspect, if one or more genes selected from Table 13 or 16 include B2M, HLA-DRA, HLA-DRB1 and/or HLA-DPA1, at least one additional gene from Table 13 or 16 is selected.

[0177] For convenience, the meaning of some terms and phrases used in the descriptive report, examples and appended claims are provided below. Unless otherwise indicated, or implied from the context, the following terms and phrases include the meanings given below. Definitions are provided to assist in describing particular embodiments and are not intended to limit the claimed invention, as the scope of the invention is limited only by the claims.

Unless defined otherwise, all technical and scientific terms used herein have the same meaning as commonly understood by those skilled in the art to which this invention belongs. If there is an evident discrepancy between the use of a term in the art and its definition given in this document, the definition given in the descriptive report shall prevail.

[0178] For convenience, certain terms used in this document, the descriptive report, examples and attached claims are compiled here.

[0179] As used herein, the term "cancer" broadly refers to a class of diseases or conditions in which abnormal cells divide uncontrollably and can invade nearby tissues. Cancer cells can also spread to other parts of the body through the blood and lymph systems. There are several main types of cancer. Carcinoma is a cancer that starts in the skin or in the tissues that line or cover the internal organs. Sarcoma is a cancer that starts in bone, cartilage, fat, muscle, blood vessels, or other connective or supportive tissue. Leukemia is a cancer that starts in blood-forming tissue, such as bone marrow, and causes large numbers of abnormal blood cells to be produced and enter the blood. Lymphoma and multiple myeloma are cancers that start in the cells of the immune system. Central nervous system cancers are cancers that start in the tissues of the brain and spinal cord.

[0180] In some modalities of either aspect, cancer is a primary cancer. In some modalities of either aspect, cancer is malignant cancer. As used herein, the term "malignant" refers to a cancer in which a group of tumor cells exhibits one or more of uncontrolled growth (ie, division beyond normal limits), invasion (ie, intrusion and destruction of adjacent tissues) and metastasis (ie, spread to other places in the body via lymph or blood). As used herein, the term "metastasis" refers to the spread of cancer from one part of the body to another. A tumor formed by cells that have spread is called a "metastatic tumor" or "metastasis". The metastatic tumor contains cells similar to those of the original (primary) tumor. As used herein, the term "benign" or "non-malignant" refers to tumors that can grow larger but do not spread to other parts of the body. Benign tumors are self-limiting and usually do not invade or metastasize.

[0181] A "cancer cell" or "tumor cell" refers to an individual cell of a cancerous tissue or growth. A tumor generally refers to a swelling or lesion formed by abnormal cell growth, which may be benign, premalignant, or malignant. Most cancer cells form tumours, but some, for example in leukemia, do not necessarily form tumours.

For cancer cells that form tumors, the terms cancer (cell) and tumor (cell) are used interchangeably.

[0182] As used herein, the term "neoplasm" refers to any new and abnormal growth of tissue, for example, an abnormal mass of tissue, whose growth exceeds and is not coordinated with that of normal tissues. Thus, a neoplasm can be a benign neoplasm, a premalignant neoplasm or a malignant neoplasm.

[0183] An individual who has a cancer or a tumor is an individual with objectively measurable cancer cells present in the individual's body. Included in this definition are actively proliferating malignant cancers as well as potentially dormant tumors or micrometastases. Cancers that migrate from their original location and proliferate to other vital organs can lead to the patient's death through functional deterioration of Organs affected organs.

[0184] Examples of cancer include, but are not limited to, carcinoma, lymphoma, blastoma, sarcoma, leukemia, basal cell carcinoma, biliary tract cancer; bladder cancer; bone cancer; brain and CNS cancer; breast cancer; cancer of the peritoneum; cervical cancer; choriocarcinoma; colon and rectal cancer; connective tissue cancer; digestive system cancer; endometrial cancer; esophageal cancer; eye cancer; head and neck cancer; gastric cancer (including gastrointestinal cancer); glioblastoma (GBM); liver carcinoma; hepatoma; intraepithelial neoplasia; kidney or kidney cancer; laryngeal cancer; leukemia; liver cancer; lung cancer (eg, small cell lung cancer, non-small cell lung cancer, lung adenocarcinoma, and squamous cell carcinoma of the lung); lymphoma, including Hodgkin's and non-Hodgkin's lymphoma; melanoma; myeloma; neuroblastoma; oral cavity cancer (eg, lip, tongue, mouth, and pharynx); Ovary cancer; pancreatic cancer; prostate cancer; retinoblastoma; rhabdomyosarcoma; rectal cancer; respiratory system cancer; salivary gland carcinoma; sarcoma; skin cancer; squamous cell cancer; stomach cancer; testicular cancer; thyroid cancer; uterine or endometrial cancer; urinary system cancer; vulvar cancer; as well as other carcinomas and sarcomas; as well as B-cell lymphoma (including low-grade/follicular non-Hodgkin's lymphoma (NHL); small lymphocytic NHL (SL); intermediate-grade/follicular NHL; intermediate-grade diffuse NHL; high-grade immunoblastic NHL; high-grade; high-grade small cell uncleaved NHL; bulky disease NHL; mantle cell lymphoma; AIDS-related lymphoma; and Waldenstrom's macroglobulinemia; chronic lymphocytic leukemia (CLL); acute lymphoblastic leukemia (ALL); hairy cells, chronic myeloblastic leukemia, and post-transplant lymphoproliferative disorder (PTLD), as well as abnormal vascular proliferation associated with phacomatoses, edema (such as that associated with brain tumors), and Meigs syndrome.

[0185] A "cancer cell" is a cancer cell, precancerous or transformed, whether in vivo, ex vivo or in tissue culture, that has spontaneous or induced phenotypic changes that do not necessarily involve the uptake of new genetic material. Although transformation can arise from infection with a transforming virus and incorporation of new genomic nucleic acid or uptake of exogenous nucleic acid, it can also arise spontaneously or after exposure to a carcinogen, thus causing a mutation in an endogenous gene. Transformation/cancer is associated, for example, with morphological changes, cell immortalization, aberrant growth control, foci formation, anchorage independence, malignancy, loss of contact inhibition and growth density limitation, serum growth or independence, tumor-specific markers, invasiveness or metastasis, and tumor growth in suitable host animals, such as nude mice.

[0186] The terms "decrease", "reduced", "reduce" or "inhibit" are all used herein to mean a decrease by a statistically significant amount. In some modalities, "reduce", "reduce" or "decrease" or "inhibit" usually means a decrease of at least 10% compared to a reference level (eg, the absence of a certain treatment or agent) and may include , for example, a decrease of at least about 10%, at least about

20%, at least about 25%, at least about 30%, at least about 35%, at least about 40%, at least about 45%, at least about 50%, at least about 55 %, at least about 60%, at least about 65%, at least about 70%, at least about 75%, at least about 80%, at least about 85%, at least about 90% , at least about 95%, at least about 98%, at least about 99% or more. As used herein, "reduction" or "inhibition" does not encompass complete inhibition or reduction compared to a reference level.

"Complete inhibition" is 100% inhibition compared to a reference level. A decrease may preferably be up to a level accepted as being within the normal range for an individual without a particular disorder.

[0187] The terms "increased", "increase", "improve" or "activate" are all used herein to mean an increase by a statically significant amount. In some modalities, the terms "increased", "increased", "improved" or "activate" may mean an increase of at least 10% compared to a reference level, for example, an increase of at least about 20%, or at least about 30%, or at least about 40%, or at least about 50%, or at least about 60%, or at least about 70%, or at least about 80%, or at least about minus about 90% or up to and including a 100% increase or any increase between 10-100% compared to a reference level, or an increase of at least about 2-fold, or at least about 3-fold, or at least about 4-fold less, or at least about 5-fold, or at least about 10-fold, or any increase between 2-fold and 10-fold or more compared to a reference level. In the context of a marker or symptom, an "increase" is a statistically significant increase in this level.

[0188] As used herein, an "individual" means a human or animal. Typically, the animal is a vertebrate, such as a primate, rodent, domestic animal or game animal. Primates include chimpanzees, cynomolgus monkeys, spider monkeys and tamarins, eg Rhesus. Rodents include mice, rats, marmots, ferrets, rabbits and hamsters. Domestic and game animals include cows, horses, pigs, deer, bison, buffalo, feline species eg domestic cat, canine species eg dog, fox, wolf, avian species eg chicken, rhea, ostrich and fish, for example, trout, catfish and salmon. In some embodiments, the individual is a mammal, eg, a primate, eg, a human. The terms, "individual", "patient"

and "person" are used interchangeably throughout this document.

[0189] Preferably, the individual is a mammal. The mammal can be a human, non-human primate, mouse, rat, dog, cat, horse or cow, but is not limited to these examples. Mammals other than humans can be advantageously used as individuals representing animal models of bronchial premalignant lesions. An individual can be a man or a woman.

[0190] An individual may be one who has been previously diagnosed or identified as suffering from or having a condition that needs treatment (eg, premalignant bronchial lesions) or one or more complications related to such a condition and, optionally, has already undergone treatment for premalignant bronchial injuries or one or more complications related to premalignant bronchial injuries. Alternatively, an individual may also be one who has not previously been diagnosed as having premalignant bronchial lesions or one or more complications related to premalignant bronchial lesions. For example, an individual may be one who exhibits one or more risk factors for premalignant bronchial lesions or one or more complications related to premalignant bronchial lesions, or an individual who does not exhibit risk factors.

[0191] An "individual in need" of treatment for a particular condition may be an individual who has such a condition, diagnosed as having such a condition or at risk of developing such a condition.

[0192] As used herein, the terms "protein" and "polypeptide" are used interchangeably herein to designate a series of amino acid residues, connected to each other by peptide bonds between the alpha-amino and carboxy residue groups adjacent. The terms "protein" and "polypeptide" refer to a polymer of amino acids, including modified amino acids (eg, phosphorylated, glycosylated, aglycosylated, etc.) and amino acid analogs, regardless of their size or function. "Protein" and "polypeptide" are often used in reference to relatively large polypeptides, while the term "peptide" is often used in reference to small polypeptides, however, the use of these terms in the art overlaps. The terms "protein" and "polypeptide" are used interchangeably herein when referring to a gene product and fragments thereof. Thus, exemplary polypeptides or proteins include gene products, naturally occurring proteins, homologs,

orthologs, paralogs, fragments and other equivalents, variants, fragments and analogues of the above.

[0193] In the various modalities described in this document, variants (naturally occurring or otherwise), alleles, homologs, conservatively modified variants and/or conservative substitution variants of any of the polypeptides are also considered to be included. described. As for amino acid sequences, those skilled in the art will recognize that individual substitutions, deletions or additions to a nucleic acid, peptide, polypeptide or protein sequence that exchanges a single amino acid or a small percentage of amino acids in the encoded sequence is a "modified variant conservatively", in which the alteration results in the replacement of an amino acid with a chemically similar amino acid and retains the desired activity of the polypeptide. These conservatively modified variants are in addition to and do not exclude polymorphic variants, interspecies homologs and alleles consistent with the invention.

[0194] A given amino acid can be replaced by a residue with similar physicochemical characteristics, for example, by replacing an aliphatic residue with another (such as Ile, Val, Leu or Ala for one another) or by replacing a polar residue on the other (such as between Lys and Arg; Glu and Asp; or Gln and Asn). Other conservative substitutions, for example, substitutions of entire regions with similar hydrophobicity characteristics, are well known. Polypeptides comprising conservative amino acid substitutions can be tested in any of the assays described herein to confirm that a desired activity, for example, the activity and specificity of a native or reference polypeptide, is retained.

[0195] Amino acids can be grouped according to similarities in the properties of their side chains (in AL Lehninger, in Biochemistry, second ed., pages 73-75, Worth Publishers, New York (1975)): (1) non-polar : Ala (A), Val (V), Leu (L), Ile (I), Pro (P), Phe (F), Trp (W), Met (M); (2) uncharged polar: Gly (G), Ser (S), Thr (T), Cys (C), Tyr (Y), Asn (N), Gln (Q); (3) acid: Asp (D), Glu (E); (4) basic: Lys (K), Arg (R), His (H).

Alternatively, naturally occurring residues can be divided into groups based on common side chain properties: (1) hydrophobic: Norleucine, Met, Ala, Val, Leu, Ile; (2) neutral hydrophilic: Cys, Ser, Thr, Asn, Gln; (3) acids: Asp, Glu; (4) basic: His, Lys, Arg; (5) residues that influence chain orientation: Gly, Pro;

(6) aromatics: Trp, Tyr, Phe. Non-conservative substitutions will imply exchanging a member of one of these classes for another class. Particular conservative substitutions include, for example; Ala by Gly or by Ser; Arg for Lys; Asn by Gln or by His; Asp for Glu; Cys for Ser; Gln for Asn; Glu by Asp; Gly by Ala or Pro; His by Asn or by Gln; Ile by Leu or by Val; Read by Ile or by Val; Lys by Arg, by Gln or by Glu; Met by Leu, by Tyr or by Ile; Phe by Met, by Leu or by Tyr; Be by Thr; Thr for Ser; Trp by Tyr; Tyr by Trp; and/or Phe by Val, by Ile or by Leu.

[0196] In some embodiments, the polypeptide described herein (or a nucleic acid encoding such a polypeptide) may be a functional fragment of one of the amino acid sequences described herein.

As used herein, a "functional fragment" is a fragment or segment of a peptide that retains at least 50% of the activity of the wild-type reference polypeptide according to the assays described herein below. A functional fragment may comprise conservative substitutions for the sequences described herein.

[0197] In some embodiments, the polypeptide described herein may be a variant of a sequence described herein. In some embodiments, the variant is a conservatively modified variant.

Conservative substitution variants can be obtained through mutations of native nucleotide sequences, for example. A "variant", as recited herein, is a polypeptide substantially homologous to a native or reference polypeptide, but which has an amino acid sequence different from that of the native or reference polypeptide by virtue of one or a plurality of deletions, insertions or replacements. DNA sequences encoding variant polypeptides encompass sequences that comprise one or more nucleotide additions, deletions or substitutions as compared to a native or reference DNA sequence, but which encode a variant protein or fragment thereof that retains activity. A wide variety of site-specific mutagenesis PCR approaches are known in the art and can be applied by those skilled in the art.

[0198] A variant amino acid sequence or DNA may be at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97 %, at least 98%, at least 99% or more identical to a native or reference sequence. The degree of homology (percentage of identity) between a native and a mutant sequence can be determined, for example, by comparing the two sequences using freely available computer programs commonly employed for this purpose on the worldwide web (eg BLASTp or BLASTn with settings pattern).

[0199] Changes to the native amino acid sequence can be made by any of a number of techniques known to those skilled in the art. Mutations can be introduced, for example, at particular loci by synthesizing oligonucleotides that contain a mutant sequence, flanked by restriction sites that allow binding to fragments of the native sequence.

After ligation, the resulting reconstructed sequence encodes an analog that has the desired amino acid insertion, substitution or deletion. Alternatively, oligonucleotide site-specific mutagenesis procedures can be employed to provide an altered nucleotide sequence with specific codons altered according to the necessary substitution, deletion or insertion. Techniques for making such changes are very well established and include, for example, those described by Walder et al.

(Gene 42:133, 1986); Bauer et al. (Gene 37:73, 1985); Craik (BioTechniques, January 1985, 12-19); Smith et al.

(Genetic Engineering: Principles and Methods, Plenum Press,

1981); and U.S. Patent Nos. 4,518,584 and 4,737,462, which are incorporated herein by reference in their entirety. Any cysteine residue not involved in maintaining the proper conformation of the polypeptide can also be substituted, usually with serine, to improve the oxidative stability of the molecule and avoid aberrant crosslinking. On the other hand, cysteine bond(s) may be added to the polypeptide to improve its stability or facilitate oligomerization.

[0200] As used herein, the term "nucleic acid" or "nucleic acid sequence" refers to any molecule, preferably a polymeric molecule, that incorporates ribonucleic acid units, deoxyribonucleic acids or an analogue thereof. Nucleic acid can be single or double stranded. A single stranded nucleic acid can be a nucleic acid strand of denatured double stranded DNA. Alternatively, it can be a single-stranded nucleic acid not derived from any double-stranded DNA. In one aspect, the nucleic acid can be DNA. In another aspect, the nucleic acid can be RNA. Suitable DNA can include, for example, genomic DNA or cDNA. Suitable RNA can include, for example, mRNA.

[0201] The term "expression" refers to the cellular processes involved in the production of RNA and proteins and, as appropriate, secretory proteins, including, where applicable, but not limited to, for example, transcription, transcription processing, translation and folding of protein, modification and processing. Expression may refer to the transcription and stable accumulation of derivatives of a fragment or fragments of the sense nucleic acid (mRNA) or antisense RNA of the invention and/or the translation of mRNA into a polypeptide.

[0202] In some embodiments, the expression of (a) biomarker(s), target(s) or gene(s)/polypeptide(s) described herein is tissue-specific.

In some embodiments, expression of (a) biomarker(s), target(s), or gene(s)/polypeptide(s) described herein is global. In some embodiments, expression of (a) biomarker(s), target(s), or gene(s)/polypeptide(s) described herein is systemic.

[0203] "Expression products" include RNA transcribed from a gene and polypeptides obtained through translation of mRNA transcribed from a gene. The term "gene" means the nucleic acid sequence that is transcribed (DNA) into RNA in vitro or in vivo when operably linked to appropriate regulatory sequences.

The gene may or may not include regions anterior and posterior to the coding region, for example, 5' untranslated sequences (5'UTR) or "leader" sequences and 3' UTR or "trailer" sequences, as well as intervening sequences (introns) between individual encoder segments (exons).

[0204] "Marker", in the context of the present invention, refers to an expression product, for example, nucleic acid or polypeptide, that is differentially present in a sample taken from individuals with pre-malignant bronchial lesions of a particular compared subtype with a comparable sample drawn from control individuals (eg, a healthy individual). The term "biomarker" is used interchangeably with the term "marker".

[0205] In some embodiments, the methods described in this document refer to measuring, detecting or determining the level of at least one marker. As used herein, the term "detection" or "measurement" refers to observing a signal, for example, from a probe, label or target molecule to indicate the presence of an analyte in a sample. Any method known in the art to detect a particular marker portion can be used for detection. Exemplary detection methods include, but are not limited to, spectroscopic, fluorescent, photochemical, biochemical,

immunochemical, electrical, optical or chemical. In some modalities of either aspect, the measurement can be a quantitative observation.

[0206] As used herein, the terms "treat", "treatment", "treated" or "improvement" refer to therapeutic treatments, where the goal is to reverse, alleviate, improve, inhibit, slow or stop progression or severity of a condition associated with a disease or disorder, for example, pre-malignant bronchial lesions. The term "treating" includes reducing or alleviating at least one adverse effect or symptom of a condition, disease or disorder associated with a premalignant bronchial lesion.

Treatment is usually "effective" if one or more symptoms or clinical markers are reduced. Alternatively, treatment is "effective" if the progression of a disease is slowed or stopped. That is, "treatment" includes not only improvement in symptoms or markers, but also cessation, or at least deceleration, of the progression or worsening of symptoms compared to what would be expected in the absence of treatment. Beneficial or desired clinical outcomes include, but are not limited to, relief of one or more symptoms, decreased disease extent, stabilized disease state (ie, no worsening), delay or deceleration of disease progression, improvement or palliation of the disease state, remission (partial or total) and/or decrease in mortality, detectable or undetectable. The term "treatment" of an illness also includes the alleviation of symptoms or side effects of the illness (including palliative treatment).

[0207] As used herein, the term "pharmaceutical composition" refers to the active agent in combination with a pharmaceutically acceptable carrier, for example, a carrier commonly used in the pharmaceutical industry. The phrase "pharmaceutically acceptable" is used herein to refer to those compounds, materials, compositions and/or dosage forms that are, within the scope of sound medical judgment, suitable for use in contact with the tissues of humans and animals. no toxicity, irritation, excessive allergic response, or other measurable problem or complication with a reasonable risk/benefit ratio. In some embodiments of either aspect, a pharmaceutically acceptable carrier may be a carrier other than water. In some embodiments of either aspect, a pharmaceutically acceptable carrier can be a cream, emulsion, gel, liposome, nanoparticle and/or ointment. In some embodiments of either aspect, a pharmaceutically acceptable carrier may be an artificial or engineered carrier, for example, a carrier whose active ingredient would not occur in nature.

[0208] As used herein, the term "administration" refers to the placement of a compound, as described herein, into an individual via a method or route that results in at least partial delivery of the agent to a desired location. . Pharmaceutical compositions comprising the compounds described herein may be administered via any appropriate route that results in effective treatment for the individual. In some embodiments, administration comprises a human physical activity, for example, an injection, an act of ingestion, an act of applying and/or manipulating a dispensing device or machine. Such activity can be carried out, for example, by a medical professional and/or the individual to be treated.

[0209] As used herein, "contact" refers to any suitable means to deliver or expose an agent to at least one cell. Exemplary delivery methods include, but are not limited to, direct delivery to cell culture media, perfusion, injection, or other delivery method well known to those skilled in the art. In some modalities, contact comprises a human physical activity, for example, an injection; an act of distribution, mixing and/or decanting; and/or manipulation of a dispensing device or machine.

[0210] As used herein, the term "inhibitor" refers to an agent that can decrease the expression and/or activity of the target molecule or activity or process, for example, by at least 10% or more, for example, 10% or more, 50% or more, 70% or more, 80% or more, 90% or more, 95% or more, or 98% or more.

[0211] As used herein, the terms "drug", "compound" or "agent" are used interchangeably and refer to molecules and/or compositions. Compounds/agents include, but are not limited to, chemical compounds and mixtures of chemical compounds, for example, small organic or inorganic molecules; saccharin; oligosaccharides; polysaccharides; biological macromolecules, for example, peptides, proteins and peptide analogues and derivatives; peptidomimetics; nucleic acids; nucleic acid analogues and derivatives; extracts made from biological materials such as bacteria, plants, fungi or animal cells or tissues; naturally occurring or synthetic compositions; peptides; aptamers; and antibodies and intrabodies, or fragments thereof. In some embodiments, "drug" as used herein refers to an agent approved for medical use, for example, by the FDA.

[0212] The term "statistically significant" or "significantly" refers to statistical significance and generally means a standard deviation of two (2SD) or a greater difference.

[0213] Except for the operational examples, or where otherwise indicated, all numbers expressing amounts of ingredients or reaction conditions used herein are to be understood as modified, in all cases, by the term "about". The term "about", when used in relation to percentages, can mean ± 1%.

[0214] As used herein, the term "comprises" means that other elements may also be present in addition to the defined elements shown.

The use of "comprises" indicates inclusion rather than limitation.

[0215] The term "consisting of" refers to compositions, methods and respective components, as described herein, which are exclusive of any element not mentioned in this modality description.

[0216] As used in this document, the term "consisting essentially of" refers to the elements necessary for a particular modality. The term allows for the presence of additional elements that do not materially affect the basic and new or functional characteristics of this embodiment of the invention.

[0217] The singular terms "a", "an" and "the" include plural references unless the context clearly indicates otherwise. Likewise, the word "or" is intended to include "and" unless the context clearly indicates otherwise. While methods and materials similar or equivalent to those described herein can be used in practicing or testing the present invention, suitable methods and materials are described below. The abbreviation, "e.g." is derived from the Latin exempli gratia and is used herein to indicate a non-limiting example. Thus, the abbreviation "e.g." is synonymous with the term "for example".

[0218] The groupings of alternative elements or embodiments of the invention described herein are not to be construed as limitations. Each group member may be cited and claimed individually or in any combination with other group members or other elements found herein. One or more members of a group may be included or excluded from a group for reasons of convenience and/or patentability. When any inclusion or exclusion occurs, the descriptive report is considered herein to contain the modified group, thus satisfying the written description of all Markush groups used in the appended claims.

[0219] Unless otherwise defined herein, scientific and technical terms used in connection with this application shall have the meanings that are commonly understood by those of ordinary skill in the art to which the present invention belongs. It should be understood that the present invention is not limited to the particular methodology, protocols and reagents etc. described herein and as such may vary. The terminology used herein is for the purpose of describing particular embodiments only and is not intended to limit the scope of the present invention, which is defined only by the claims. Definitions of common terms in immunology and molecular biology can be found in The Merck Manual of Diagnosis and Therapy, 20th Edition, published by Merck Sharp & Dohme Corp., 2018 (ISBN 0911910190, 978-0911910421); Robert S. Porter et al. (eds.), The Encyclopedia of Molecular Cell Biology and Molecular Medicine, published by Blackwell Science Ltd., 1999-2012 (ISBN 9783527600908); and Robert A. Meyers (ed.), Molecular Biology and Biotechnology: a Comprehensive Desk Reference, published by VCH Publishers, Inc., 1995 (ISBN 1-56081-569-8); Immunology by Werner Luttmann, published by Elsevier, 2006; Janeway's Immunobiology, Kenneth Murphy, Allan Mowat, Casey Weaver (eds.), W.W. Norton & Company, 2016 (ISBN 0815345054, 978-0815345053); Lewin Genes XI, published by Jones & Bartlett Publishers, 2014 (ISBN-1449659055); Michael Richard Green and Joseph Sambrook, Molecular Cloning: A Laboratory Manual, 4th ed., Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y., USA (2012) (ISBN 1936113414); Davis et al., Basic Methods in Molecular Biology, Elsevier Science Publishing, Inc., New York, USA (2012) (ISBN 044460149X); Laboratory Methods in Enzymology: DNA, Jon Lorsch (ed.) Elsevier, 2013 (ISBN 0124199542); Current Protocols in Molecular Biology (CPMB), Frederick M. Ausubel (ed.), John Wiley and Sons, 2014 (ISBN 047150338X, 9780471503385), Current Protocols in Protein Science (CPPS), John E. Coligan (ed.), John Wiley and Sons, Inc., 2005; and Current Protocols in Immunology (CPI) (John E. Coligan, ADA M Kruisbeek, David H Margulies, Ethan M Shevach, Warren Strobe, (eds.) John Wiley and Sons, Inc., 2003 (ISBN 0471142735, 9780471142737), the contents all of which are incorporated by reference into this document in its entirety.

[0220] Other terms are defined herein within the description of the various aspects of the invention.

[0221] All patents and other publications; including literature references, granted patents, published patent applications and co-pending patent applications cited throughout this application are expressly incorporated herein by reference for the purpose of describing and disclosing, for example, the methodologies described in such publications that can be used in association with the technology described in this document. These publications are provided for your description only prior to the filing date of this order. Nothing in this regard should be construed as an admission that inventors are not entitled to advance such disclosure by virtue of prior invention or for any other reason. All statements as to the date or representation as to the content of these documents are based on the information available to applicants and do not constitute an admission as to the accuracy of the dates or content of these documents.

[0222] The description of the embodiments of the invention is not intended to be exhaustive or to limit the invention to the precise form described. While specific embodiments and examples of the invention are described herein for illustrative purposes, various equivalent modifications are possible within the scope of the invention, as those skilled in the relevant art will recognize. For example, although method steps or functions are presented in a certain order, alternative modalities may perform functions in a different order, or the functions may perform substantially simultaneously. The teachings of the invention provided herein can be applied to other procedures or methods as appropriate. The various modalities described in this document can be combined to provide other modalities. Aspects of the invention may be modified, if necessary, to employ the compositions, functions and concepts of the above references and applications to provide still other embodiments of the invention. These and other changes can be made to the invention in light of the detailed description.

All such modifications must be included within the scope of the appended claims.

[0223] Specific elements of any of the previous modalities can be combined or replaced by elements in other modalities. Furthermore, while advantages associated with certain embodiments of the invention have been described in the context of these embodiments, other embodiments may also exhibit such advantages, and not all embodiments need necessarily exhibit such advantages to be within the scope of the invention.

[0224] The technology described in this document is further illustrated by the following examples, which in no way should be interpreted as being limiting.

[0225] Some modalities of the technology described in this document may be defined in accordance with any of the following numbered paragraphs:

1. A method of treating bronchial premalignant lesions comprising: administering at least one of: a bronchoscopy-based procedure to examine the central airway and a computed tomography scan of the chest; at least every 6 months, one of a bronchoscopy-based procedure to examine the central airway and a chest CT scan; and/or at least one antiproliferative drug; to an individual determined to have at least one of: an increased expression level of at least one module 5 gene compared to a reference level of non-proliferative lesion; and a reduced expression level of at least one module 6 gene compared to a reference level of non-proliferative lesion.

2. Method according to item 1, wherein the at least one gene from module 5 is selected from the group consisting of: RACGAP1 and TPX2; and at least one of the module 6 gene is selected from the group consisting of: NEK11 and IFT88.

3. The method according to any one of items 1-2, wherein the individual is further determined to have an increased expression level of at least one module 7 gene or module 4 gene.

4. Method according to item 3, wherein at least one of the module 7 or module 4 gene is selected from the group consisting of: COX6A1; COX7A2; RPL26; and RPL23.

5. Method according to any one of items 1-4, wherein the expression level of each of the genes in Table 15 is determined.

6. The method according to any one of items 1-5, wherein the at least one antiproliferative drug is selected from the group consisting of: Acetylcholine receptor antagonists; Acetylcholinesterase inhibitors; Adenosine receptor antagonists; Adrenergic receptor antagonists; AKT Inhibitors;

Angiotensin receptor antagonists; Apoptosis stimulants; Aurora kinase inhibitors; CDK Inhibitors;

Cyclooxygenase inhibitors; Inhibitors of cytokine production; Dehydrogenase Inhibitors; DNA protein kinase inhibitors; Focal adhesion inhibitors;

Dopamine receptor antagonists; EGFR Inhibitors;

ERK1 and ERK2 phosphorylation inhibitors; Estrogen receptor agonists; EZH2 Inhibitors; FLT3 Inhibitors;

Glucocorticoid receptor agonists; Glutamate receptor antagonists; HDAC inhibitors; Histamine Receptor Antagonists; Histone Lysine Methyltransferase Inhibitors; HSP Inhibitors; IKK inhibitors;

Ion channel antagonists; JAK inhibitors; Inhibitors

JNK; KIT inhibitors; Leucine-rich repeat kinase inhibitors; MDM Inhibitors; Inhibitors of mediator release; MEK Inhibitors; MTOR inhibitors;

Monoamine oxidase inhibitors; NFB pathway inhibitors;

Nucleophosmin Inhibitors; PARP inhibitors; PPAR receptor agonists; PI3K inhibitors; Tyrosine kinase inhibitors; Phosphodiesterase Inhibitors; Protein kinase inhibitors; RAF inhibitors; RNA polymerase inhibitors; topoisomerase inhibitors; RNA synthesis inhibitors; SIRT Inhibitors; Sodium channel blockers; VEGFR Inhibitors; and Vitamin D receptor agonists.

7. The method according to any one of items 1-6, wherein the anti-proliferative drug is administered as an inhaled formulation or topical formulation.

8. Method according to any one of items 1-7, wherein the antiproliferative drug is administered during a bronchoscopy-based procedure.

9. Method according to any one of items 1-8, wherein the antiproliferative drug is administered systemically.

10. Method according to any one of items 1-9, wherein the antiproliferative drug is administered during a bronchoscopy-based procedure and systemically.

11. Method according to any one of items 1-10, wherein the subject is further determined to have a reduced expression level of at least one module 9 gene compared to a reference level of non-proliferative lesion and/or a increased expression level of at least one module 10 gene compared to a reference level of non-proliferative lesion.

12. Method according to item 11, wherein the individual determined to have a reduced expression level of at least one module 9 gene and/or an increased expression level of at least one module 10 gene receives at least one of: either a bronchoscopy-based procedure to examine the central airway in which lesions are biopsied to remove abnormal tissue or a CT scan of the chest; at least every 6 months, one of a bronchoscopy-based procedure to examine the central airway in which lesions undergo biopsy to remove abnormal tissue and a chest CT scan; and/or at least one immunostimulating drug.

13. Method of treatment of premalignant bronchial lesions characterized by comprising: administering at least one of: either a bronchoscopy-based procedure to examine the central airway in which lesions are biopsied to remove the abnormal tissue or a CT scan chest computerized; at least every 6 months, one of a bronchoscopy-based procedure to examine the central airway in which lesions undergo biopsy to remove abnormal tissue and a chest CT scan; and/or at least one immunostimulating drug;

to an individual determined to have a reduced expression level of at least one module 9 gene compared to a non-proliferative lesion reference level and/or an increased expression level of at least one module 10 gene compared to a level of reference of non-proliferative lesion.

14. Method according to any one of items 11-13, wherein the module 9 gene is selected from the group consisting of: EPSTI1; UBE2L6; B2M and TAP1.

15. Method according to any one of items 11-14, wherein at least one gene from module 9 is selected from Table 16.

16. Method according to any one of items 11-15, wherein the module 10 gene is selected from the group consisting of: CACNB3 and MAPK10.

17. Method according to any one of items 11-16, wherein the at least one immunostimulating drug is selected from the group consisting of: Immune checkpoint inhibitors (eg, inhibitors against PD-1, PD- L1, CTLA4 and LAG3); Drugs that stimulate interferon signaling (eg, antiviral drugs that improve interferon signaling);

DNA synthesis inhibitors; IMDH inhibitors; CDK Inhibitors; Ribonucleotide reductase inhibitors; Dihydrofolate reductase inhibitors; topoisomerase inhibitors; FLT3 Inhibitors; IGF-1 Inhibitors; MEK Inhibitors; Aurora kinase inhibitors; PKC Inhibitors; RAF inhibitors; PDFGR/KIT inhibitors; VEGFR Inhibitors; SRC inhibitors; Retinoid receptor agonists; HDAC inhibitors; DNA methyltransferase inhibitors; and EZH2 Inhibitors.

18. A method of treating bronchial premalignant lesions comprising: administering at least one of: a bronchoscopy-based procedure to examine the central airway and a computed tomography scan of the chest; at least every 6 months, one of a bronchoscopy-based procedure to examine the central airway and a chest CT scan; and/or at least one anti-inflammatory; to an individual determined to have at least one of: an increased expression level of at least one module 2 gene compared to a non-inflammatory reference level; and a reduced expression level of at least one module 6 gene compared to a non-inflammatory reference level.

19. Method according to item 17, wherein the at least one module 2 gene is selected from the group consisting of: MSANTD2, CCNL2 and LUC7L; and at least one of the module 6 gene is selected from the group consisting of: NEK11 and IFT88.

20. The method according to any one of items 17-18, wherein the individual is further determined to have an increased expression level of at least one module 7 gene, module 1 gene or module 8 gene and/or level of reduced expression of in at least one module 4 gene or one module 5 gene.

21. Method according to item 19, wherein at least one of the module 7 gene is selected from the group consisting of: RPL26 and RPL23.

22. Method according to item 19, wherein at least one of the module 1 gene is selected from the group consisting of: KIRREL; PHLDB1; and MARVELD1.

23. Method according to item 19, wherein at least one module 8 gene is selected from the group consisting of: DOC2; CD53; and LAPTM.

24. Method according to item 19, in which at least one of the module 4 gene is selected from the group consisting of: COX6A1 and COX7A2

25. Method according to item 19, wherein at least one of the module 5 gene is selected from the group consisting of: RACGAP1 and TPX2

26. Method according to any one of items 17-24, in which the expression level of each of the genes in Table 15 is determined.

27. The method according to any one of items 17-25, wherein at least one of the anti-inflammatory drug is selected from the group consisting of: Acetylcholine receptor antagonists; Acetylcholinesterase inhibitors; Adenosine receptor antagonists; Adrenergic receptor antagonists; AKT Inhibitors; Angiotensin receptor antagonists; Apoptosis stimulants; Aurora kinase inhibitors; CDK Inhibitors; Cyclooxygenase inhibitors; Inhibitors of cytokine production; Dehydrogenase Inhibitors; DNA protein kinase inhibitors; Focal adhesion inhibitors; Dopamine receptor antagonists; EGFR Inhibitors;

ERK1 and ERK2 phosphorylation inhibitors; Estrogen receptor agonists; EZH2 Inhibitors; FLT3 Inhibitors; Glucocorticoid receptor agonists; Glutamate receptor antagonists; HDAC inhibitors; Histamine Receptor Antagonists; Histone Lysine Methyltransferase Inhibitors; HSP Inhibitors; IKK inhibitors; Ion channel antagonists; JAK inhibitors; JNK inhibitors; KIT inhibitors; Leucine-rich repeat kinase inhibitors; MDM Inhibitors; Inhibitors of mediator release; MEK Inhibitors; MTOR inhibitors; Monoamine oxidase inhibitors; NFB pathway inhibitors; Nucleophosmin Inhibitors; PARP inhibitors; PPAR receptor agonists; PI3K inhibitors; Tyrosine kinase inhibitors; Phosphodiesterase Inhibitors; Protein kinase inhibitors; RAF inhibitors; RNA polymerase inhibitors; topoisomerase inhibitors; RNA synthesis inhibitors; SIRT Inhibitors; Sodium channel blockers; VEGFR Inhibitors; and Vitamin D receptor agonists.

28. Method according to any one of items 17-26, wherein the anti-inflammatory drug is administered during a bronchoscopy-based procedure.

29. Method according to any one of items 17-27, wherein the anti-inflammatory drug is administered systemically.

30. Method according to any one of items 17-28, wherein the anti-inflammatory drug is administered during a bronchoscopy-based procedure and systemically.

31. Method according to any of items 1-29, wherein at least one of the gene is selected from Table

14.

32. Method according to any one of items 1-30, wherein the expression level of each of the genes in Table 14 is determined.

33. Method according to any one of items 1-31, wherein the development of lung cancer, squamous cell carcinoma of the lung is prevented, delayed or diminished.

34. Method according to any of items 1-32, where lung cancer is squamous cell carcinoma of the lung.

35. Method according to any of items 1-33, where the expression level is the expression level in an endobronchial biopsy, endobronchial smear sample, upper airway biopsy, upper airway smear sample, cells nasal epithelial cells, sputum, or blood obtained from the individual.

36. Method according to any of items 1-34, where expression level is the expression level in a bronchial smear taken from the right or left main bronchus.

37. Method according to any one of items 34-35, wherein the biopsy or smear sample comprises morphologically normal tissue or cells.

38. Method according to any of items 34-35, wherein the biopsy or smear sample consists of morphologically normal tissues or cells.

39. The method according to any one of items 1-34, wherein the expression level is the expression level in a sample comprising bronchial premalignant lesion cells.

40. Method according to any one of items 1-35, wherein the expression level is the expression level in a sample comprising morphologically normal cells.

41. Method according to any one of items 1-36, where the individual is a smoker or ex-smoker.

EXAMPLES

Example 1: Molecular subtyping reveals immune changes associated with the progression of premalignant bronchial lesions

[0226] Described here is the molecular characterization of premalignant bronchial lesions and the epithelial and immune changes identified in the field of airway injury associated with progressive/persistent bronchial dysplasia that can be leveraged to develop risk biomarkers and interception strategies in lung cancer.

[0227] Bronchial premalignant lesions (PMLs) are precursors of squamous cell carcinoma of the lung, but they have variable outcomes and lack tools to identify and treat PMLs with increased risk of progression to invasive cancer. The profile of endobronchial biopsies of PMLs obtained from high-risk smokers by RNA-Seq identified four subtypes of PML with differences in epithelial and immune processes. A molecular subtype (Proliferative) is enriched with dysplastic lesions and exhibits upregulation of metabolic pathways and cell cycle and downregulation of ciliary processes. RNA-Seq profiles of normal-appearing uninvolved upper airway smears can identify individuals with proliferative lesions with high specificity. The expression of interferon signaling pathways and processing pathways/

antigen presentation is decreased in progressive/persistent proliferative lesions and immunofluorescence indicates a depletion of innate and adaptive immune cells in these lesions. Molecular biomarkers measured in PMLs or in uninvolved airways may increase histopathological grading and indicate that immunoprevention strategies may be effective in intercepting the progression of PMLs to lung cancer.

Introduction

[0228] Lung cancer (LC) is the leading cause of cancer death, taking an estimated 160,000 lives in the US each year, more than colorectal, pancreatic, breast and prostate cancers combined. In order to reduce mortality, innovative strategies are needed to intercept the development of cancer, diagnosing the disease in its early and potentially more curable stage.

Recent advances based on the results of the National Lung Screening Trial (1) are drastically changing the landscape of early detection of LC, as computerized tomography (CT) screening of high-risk individuals significantly reduces mortality. Despite this progress, biomarkers are needed to select individuals for LC screening, as eligibility criteria represent less than 27% of individuals diagnosed with LC in the US (2) and to distinguish between benign or cancerous indeterminate pulmonary nodules, a since the trace has a very high false positive rate (>90 %). There is also an urgent and unmet need to develop personalized therapies early in the disease process to "intercept" LC before it develops in this high-risk population.

[0229] The development of LC risk biomarkers and LC intercept strategies requires a detailed understanding of the earliest molecular changes involved in lung carcinogenesis that occur in the respiratory epithelium (3, 4). Exposure to cigarette smoke creates a field of injury throughout the respiratory tract, inducing a variety of genomic changes that can lead to an "at risk" airway where premalignant lesions (PMLs) and CL develop. Squamous cell carcinoma of the lung (LUSC) arises in the epithelial layer of the bronchial airways and is often preceded by the development of PMLs through a gradual histological progression from normal epithelium to hyperplasia, squamous metaplasia, dysplasia (mild, moderate and severe), carcinoma in situ (CIS), and finally to invasive and then metastatic LUSC (5). In fact, the presence of high-grade persistent or progressive dysplasia (moderate or severe) is a marker of increased risk for LC both at the site of injury (where they are the presumptive precursors of squamous cell lung cancer) and elsewhere in the lung, although many dysplastic lesions have varied results (6). Currently, however, effective tools to identify PMLs do not present an increased risk of progression to invasive carcinoma (7). The development of disease progression markers would identify high-risk patients, suggest new lung cancer chemoprevention agents, and provide molecular biomarkers to monitor outcome in lung cancer prevention studies.

[0230] It is theorized in this document that the molecular characterization of bronchial biopsies that contain a mixture of epithelial and immune cells would allow us to identify transcriptomic changes associated with high-grade histology and progression of premalignant lesion.

In this study, mRNA sequencing was used to profile endobronchial biopsies and smear obtained by serial bronchoscopy of high-risk smokers undergoing lung cancer screening using autofluorescent bronchoscopy and computed tomography of the chest. Using bronchial biopsies, four molecular subtypes associated with clinical phenotypes and biological processes were identified. A subtype (Proliferative subtype)

is enriched with biopsies with dysplastic histology, high basal cell signals and low hair cell signals and expression of pathways associated with proliferation. Genes involved in interferon signaling and T-cell mediated immunity were down-regulated between progressive/persistent lesions within the Proliferative subtype compared to regressive lesions and these pathways correlated with decreases in innate and adaptive immune cell types. Molecular classification of biopsies into a group of high-grade/progressive diseases can be used to stratify patients in prevention studies and monitor treatment effectiveness. The results also indicate that personalized lung cancer chemoprevention targeting specific cancer-related pathways or the immune system may have potential therapeutic benefits.

Results Population of Individuals

[0231] In this study, mRNA sequencing was used to profile endobronchial biopsies and smears obtained by serial bronchoscopy from high-risk smokers who underwent lung cancer screening through autofluorescence bronchoscopy and computed tomography of the chest at the Roswell Park Comprehensive Cancer Center (Roswell) in Buffalo, NY. Discovery Cohort samples were obtained from subjects at Roswell between 2010 and 2012 (DC; n = 29 patients, n = 191 biopsies, n = 91 smears) and Validation Cohort samples were obtained between 2012 and 2015 (VC; n = 20 patients, n = 111 biopsies and 49 smears). The individuals are predominantly older smokers, many of whom have a history of lung cancer, chronic obstructive pulmonary disease (COPD), and occupational exposures that carry a high risk of developing lung cancer. Clinical characteristics reported at baseline, such as sex, age, smoking (sometimes or never) reported at baseline, years of smoking, prior history of lung cancer, COPD status, and occupational exposures were not significantly different between two cohorts (Table 1). After filtering the sample based on various quality measures, CD had 190 biopsies and 89 smears, while VC had 105 biopsies and 48 smears.

Ninety-four percent of individuals had at least one lung anatomical location collected 2 or more times by endobronchial biopsy. The DC and VC contained 37.9% and 35.2% of biopsies with histological grade of dysplasia or higher and 23.1% and 19.0% with progressive/persistent dysplasia, respectively (Table 2). A previously described smoking-associated signature (8) was used to predict smoking in each sample, as smoking was only available at baseline, and DC was found to have a higher percentage of biopsies predicted to be smokers. (62.6%) compared to VC (36.2%). There is no significant difference in smoking status between the bronchial smears between the two cohorts, as only 1 smear is collected per time point. Predicted smoking status was consistent across all procedures for 63% and 70% of subjects in CD and VC, respectively. In terms of RNA sequencing quality, DC had significantly higher total reads, percent-only mapping reads, and median transcription integrity number scores among biopsies than VC, however, these differences between cohorts did not were reflected in the smears (Figure 5).

PMLs in LUSC within the discovery cohort divide into distinct molecular subtypes

[0232] In order to identify gene expression differences associated with histological severity of PMLs in LUSC using endobronchial biopsies, a discovery-based approach was used to identify de novo molecular subtypes based on distinct patterns of gene coexpression (gene modules) . The approach was chosen as there is histological heterogeneity within the biopsies and pathological analyzes were conducted using biopsies adjacent to profiled biopsies via mRNA-Seq. First, we tried to select a set of gene modules that are present in different datasets in LUSC.

Using weighted gene coexpression network analysis (9) (WGCNA), gene modules were derived from CD biopsies (n = 190 samples, n = 16653 genes, n = 15 gene modules), CD smears (n = 89 samples, n = 16058 genes, n = 47 gene modules), TCGA squamous cell carcinoma tumors (LUSC) (10) (n = 471 samples, n = 17887 genes, n = 55 gene modules) and mouse tracheobronchial samples treated with n-nitrosotris-(2-chloroethyl)urea (NTCU) (n = 25 samples, n = 14897 genes, n = 40 gene modules). CD biopsy gene modules that were highly correlated (Pearson absolute correlation coefficient r > 0.85) with at least one other non-CD biopsy module within each of the 4 data sets were selected. The genes in the selected modules were filtered, requiring that each gene also be present in at least one of the correlated non-DC biopsy modules, resulting in a set of 9 gene modules that consisted of 3936 genes in total (Figure 6).

These gene modules identified 4 molecular subtypes in CD biopsies via consensus cluster: Proliferative

(dark blue, n = 52 samples, 27.4 %), Inflammatory (dark green, n = 37 samples, 19.5%), Secretor (light blue, n = 61 samples, 32.1%) and Normal (green of course, n = 40 samples, 21.1%) (Figure 1A, Table 3).

[0233] In order to characterize each molecular subtype, the first focus was on identifying over-represented biological pathways in the genes that make up each gene module, since the expression pattern of the gene module defines each PML subtype. Each gene module was found to be associated with distinct epithelial and immune biological processes (Figure 1A, Figure 6 and Table 5). The Proliferative subtype is specifically characterized by increased expression of genes involved in energy metabolism and cell cycle pathways (Modules 4 and 5). The Secretor and Normal subtypes have increased expression of genes in cilia-associated pathways (Module 6), however, the Normal subtype has specifically decreased expression of genes involved in inflammation, lymphocyte and leukocyte regulation, and antigen processing and presentation pathways ( Modules 8 and 9). The Secretor subtype exhibits decreased expression of genes involved in protein translation (Module 7), while RNA processing genes (Module 2) are more strongly expressed in the Inflammatory subtype.

[0234] Molecular subtypes have been further characterized by their associations with clinical phenotypes and established molecular subtypes in LUSC tumor (11, 12).

The smoking status of the sample, the individual from whom the sample was derived, and the histology of the sample demonstrated significant associations with the subtype (p < 0.01, Figure 1B, Table 6, Figure 8). The Proliferative and Secretor subtypes are enriched for current smokers and this association leads to the individual's enrichment, since 79% of the individuals maintain their smoking status throughout the study.

In addition, the Proliferative subtype is enriched in biopsies with dysplasia histology (Figure 1B). The Proliferative subtype has high expression of genes involved in cell cycle processes, including the proliferation marker MKI67, which is significantly up-regulated among samples in this subtype compared to samples in other subtypes (FDR = 1.0e-30, linear model , based on differential expression analysis between samples in Proliferative versus Non-Proliferative subtypes in all genes). The gene remained significantly up-regulated in the Proliferative subtype in samples with normal histology/hyperplasia (FDR = 3.4e-10, linear model) and samples with dysplasia histology (FDR = 3.1e-8, linear model), and these observations are supported by an increase in protein expression in representative samples (p = 0.02) (Figures 1C-1E and Figure 9). Proliferative subtype samples also had high agreement with the LUSC-Classic subtype (Figure 1B). In TCGA LUSC tumors, the LUSC-Classic subtype was associated with alterations and overexpression of KEAP1 and NFE2L2, as well as 3q26 amplification with overexpression of SOX2, TP63 and PIK3CA (11). Likewise, our proliferative PMLs increased the expression of KEAP1, NFE2L2, TP63 and PIK3CA (FDR = 1.4e-6, 4.5e-12, 1.4e-9 and 0.03, respectively, linear model) (Figure 10A). Furthermore, the LUSC-Classic subtype was found to be associated with increased expression of genes involved in energy metabolism and our Proliferative subtype is in part defined by the high expression of Module 4, which is enriched in genes associated with oxidative phosphorylation and the electron transport chain. In contrast, the Inflammatory and Secretor PML subtypes demonstrate enrichment in the LUSC-Secretor subtype. The LUSC-Secretor subtype was associated with processes related to the immune response, and the Inflammatory and Secretor type PMLs have the highest expression of Module 8, which is enriched in genes in these same pathways.

[0235] Finally, the extent to which PML molecular subtypes were driven by differences in epithelial and immune cell type composition was examined by evaluating the expression of a number of canonical cell type markers. The Inflammatory and Secretor subtypes have higher levels of expression of the white blood cell marker PTPRC (CD45), consistent with enrichment in the LUSC-Secretor subtype (Figure 10B, FDR = 0.12 and 0.01, respectively, linear model). Consistent with the behavior and pathways enriched in Module 6, the expression of the hair cell marker TUB1A1 is decreased in the Inflammatory and Proliferative subtypes (FDR = 1.1e-4 and 3.5e-19, respectively, linear model), and this too is shown by a decrease in acetylated -tubulin staining in representative histological samples (Figure 1E, Figure 9).

The Proliferative subtype has the highest expression (FDR = 2.4e-15, linear model 1) of the basal cell marker (KRT5), indicating enrichment in lesions with high-grade histology that closely correlates with protein expression in samples representative histological findings (p = 0.01) (Figure 1E, Figure 9, Figure 10B, Table 7). Furthermore, gene expression of MUC5AC, a marker of goblet epithelial cells, is increased in enriched subtypes for current smokers (Proliferative and Secretor), but is more significantly increased in the Secretor subtype (FDR = 3.4e-5, linear model). In contrast,

gene expression of SCGB1A1, a goblet cell marker, is the lowest in the Proliferative subtype (FDR = 6.1e-5, linear model). The Normal subtype is supported by the expression of all epithelial cell types and has the lowest expression of CD45 (FDR = 7.6e-4, linear model).

The expression levels of these marker genes agree with cell-type deconvolution methods for examining epithelial and immune cell content (Figures 10C-10D). The sum of these characterizations highlights the cell-associated epithelial and immune pathways that are modulated by smoking and PML histology, and identifies the Proliferative subtype as a subset of high-grade PMLs that express proliferative and cell cycle-related pathways.

Phenotypic Associations With Molecular Subtypes Are Confirmed in the Validation Cohort

[0236] Next, we wanted to determine whether the heterogeneity captured in the molecular subtypes derived from the DC biopsy was reproducible in CV. A closest 22-gene centroid molecular subtype predictor was developed by selecting representative genes from each of the 9 gene modules. The predictor has 84.7% accuracy in biopsies in CD (training set, Figure 2A and Figure 11) with the following misclassification rates by subtype 5/52 (9.6%) in Proliferative, 7/37

(18.9%) in Inflammatory, 9/61 (14.8%) in Secretor and 8/40 (20%) in Normal. The 22-gene classifier was used to predict the molecular subtype of 105 VC biopsies (Figure 2B). Subtype predictions in CV were evaluated by examining the concordance of metagene scores for each of the 9 modules (using the full set of genes for each module) between the predicted CV subtypes compared to the CD subtypes. The average behavior of Principal Component 1 (PC1) across subtypes was highly similar (Figure 12), with few exceptions (namely Module 3 which had the fewest number of genes). In addition, the CV subtype predictions of the 22-gene classifier were compared to the CV biopsy-derived subtypes using the same methodology used to derive the CD subtypes and significant agreement was found (p = 1.0e-7, with the Proliferative subtype having the greatest agreement between predictions, Figure 11).

[0237] The statistical associations between CV subtypes (through the 22-gene classifier) and clinical and molecular phenotypes in CV biopsies are analogous to those observed in CD biopsies (Figure 2C, Table 6, Figure 8 and Figures 10A -10H). Briefly, the Proliferative subtype is enriched in current smokers, biopsies with dysplasia histology, and the LUSC-Classic tumor subtype

(Figure 2C, Table 6). Expression of the epithelial and white blood cell marker gene through biopsies in VC reveals higher levels of the white blood cell marker PTPRC (CD45 expression) in the Inflammatory subtype (FDR = 0.002), consistent with the enrichment of the Secretor LUSC subtype (Figure 10F ).

[0238] The Inflammatory and Proliferative subtypes reduced the expression of the hair cell marker (FOXJ1), consistent with Module 6 (FOXJ1 FDR = 0.0005 and FDR = 2.62e-6 and Module 6 FDR = 5.73e-6 and FDR = 4.34e-10, respectively). The Proliferative subtype has the highest expression of the basal cell marker KRT5 (FDR = 1.67e-7), proliferation marker MKI67 (FDR = 3.03e-10) and Module 5 associated with the cell cycle (FDR = 1.23e -18), indicating enrichment of lesions that express characteristics associated with high-grade histology. The gene expression of SCGB1A1, a goblet cell marker, is lower in the Proliferative subtype (FDR =

1.8e-4). The gene expression of MUC5AC, a marker of goblet epithelial cells, was increased in current smokers and more significantly in the Secretor subtype in CD biopsies; however, in CV biopsies, this trend is not preserved, as current smokers are not enriched in the Secretor subtype. Expression levels of these marker genes agree with other deconvolution methods to examine epithelial and immune cell content (Figures 10E-10H).

Normal-appearing airway field smears reflect the molecular subtype of the biopsy

[0239] Previously, it has been shown that bronchial smears from normal-appearing areas of the main bronchus can predict the presence of PMLs (13); however, this study did not take biopsies and smears from the same individuals. Above, in biopsies in CD and VC, the Proliferative subtype represents a distinct subtype of PMLs enriched in dysplastic histology that expresses metabolic and proliferative pathways.

Biopsies classified as the Proliferative subtype may represent a group of PMLs that require careful monitoring and intervention. As a result, we sought to explore whether or not it was possible to predict the presence of Proliferative subtype biopsies using the smears. The Proliferative subtype is defined by the behavior of Modules 4, 5, 6 and 7 (Table 3) and therefore the subset of 8 genes (from the 22-gene predictor) corresponding to these modules was used to predict the presence of the Proliferative subtype in biopsies and smears in CD and VC. Prediction of the Proliferative subtype in a smear is specific (91% and 92% in CD and VC biopsies, respectively) but not sensitive (39

% and 32% of biopsies in DC and VC, respectively) in indicating the presence of at least one proliferative PML detected at the same time point (Figure 3A). In order to understand the performance of the classifier in predicting the Proliferative subtype in smears, the Genetic Set Analysis of Variation (GSVA) scores (14) were examined for Modules 4, 5, 6, and 7, which define the Proliferative subtype in smears. smears in DC and VC (Figure 3B). In the DC and VC smears, the GSVA scores were significantly different (FDR < 0.05) in the Proliferative subtype compared to all other samples only for Modules 5 and 6 and therefore likely contribute more strongly to the Proliferative subtype classification on smears. Module 5 contains genes associated with cell cycle and proliferation, while Module 6 contains genes associated with ciliary assembly and organization.

Down-regulation of Modules 5 and 6 in the smears specifically predicts the presence of a Proliferative subtype PML; however, the absence of these signs in the field of airway injury does not prevent the development of a Proliferative subtype PML.

Genes associated with the immune system separate Progressive/Persistent PMLs from proliferative and regressive subtypes

[0240] Previous studies of bronchial PMLs suggest that high-grade lesions (which occur more frequently in current smokers) are more likely to progress to invasive carcinoma (6). Therefore, we sought to identify molecular changes associated with the subsequent progression/persistence of PML (n = 15) versus regression (n

= 15) among biopsies in CD of the Proliferative subtype, as these may be clinically relevant to identify adequate interception strategies.

Using the GSVA scores calculated on all CD biopsies for each of the 9 modules, it was calculated which scores were statistically different between progressive/persistent versus regressive disease in samples belonging to the Proliferative subtype (Figure 7). Found-

if the DC Biopsy GSVA Module scores for the

Module 9 were significantly higher among PMLs

Regressive proliferatives (p = 0.002, linear model, Figure

4A) compared to progressive/persistent Proliferative PMLs.

The association between low score for Module 9 and progression/persistence is replicated in the CV biopsies (n = 7 progressive/persistent and n = 13 regressive biopsies; p = 0.03, linear model

4B). The ability of the GSVA scores from Module 9 to discriminate between regressive versus progressive/persistent biopsies as measured by the area under the receiver operating characteristic (ROC) was 0.809 and 0.802 in the biopsies in DC and VC, respectively.

[0241] The genes in Module 9 include a series of genes that code for proteins involved in interferon signaling, as well as antigen processing and presentation (SP100, CIITA, CXCL10, SOCS1, GBP1, GBP4, B2M, TAP1, TAPBP, TRIM 14, TRIM21, TRIM22, STAT1, PML, OAS2, OAS3, MX1, ADAR, ISG15, IFI35, IFIT3, IFI27, PSMB8, PSMB9, BST2, IRF1, IRF9, CD74, PSME1, PSME2, HLA-DQA1/DPA1/DPB1/ DRA/DQB2/DRB1/DQB1/DMA/DMB/DOA, HLA-A/B/C/E/F) and include the inhibitory receptor LAG3. As a result, we wanted to assess whether the presence or absence of innate or adaptive immune cells was associated with the expression of Module 9 within the Proliferative subtype. In an effort to deconvolve the potential presence of immune cell types, GSVA scores were generated using previously described immune cell signatures (15) and scores for 64 different cell types using the xCell algorithm (16), separately for both biopsies in the DC and VC. Significant associations (FDR < 0.05) were identified between the cell type score and Module 9 that were in common between biopsies in DC and VC (Figure 13) and 8 cell types identified (via xCell), including cells dendritic cells, activated dendritic cells, plasmacytoid dendritic cells, macrophages, M1 macrophages, as well as CD8+ effector memory T cells, CD8+ central memory T cells, and regulatory T cells (Figure 4C). Together, progressive/persistent biopsies in the Proliferative subtype down-regulated Module 9 expression compared to regressive biopsies that correlate with reduced signals from innate and adaptive immune cell populations.

Immunofluorescence reveals the modulation associated with the progression of macrophages and T cells in proliferative PMLs

[0242] In order to confirm the relationship between the types of immune cells associated with Module 9 and progression/histological persistence of PMLs in the Proliferative subtype, immunofluorescent staining of macrophages/monocytes (n = 52 enumerated regions of n = 16 individuals), CD4 (n = 50 enumerated regions of n = 17 individuals) and CD8 T cells (n = 47 enumerated regions of n = 16 individuals) were performed (Table 7). The results were analyzed in all subjects tested within the Proliferative subtype and in the subset of subjects where the injury outcome (progression/persistence versus regression) was in agreement with the GSVA score from Module 9 (denoted as the concordant set). Staining of CD68, a marker of pan macrophages (and tumor-associated macrophages), suggestive of type M1 macrophages, was increased in progressive/persistent lesions (p < 0.001 in the concordant set). In contrast, staining of CD163 in combination with CD68, considered suggestive of type M2 macrophages, decreased among progressive/persistent lesions in the Proliferative subtype (p < 0.001 using all subjects and p = 0.0007 in the concordant set, respectively, model linear) (Figures 4D-4E). In addition, CD4 T cells were increased (p < 0.001 in concordant set, linear model) and CD8 T cells were decreased (p < 0.001 in concordant set) in progressing/persisting PMLs. Interestingly, among the progressive/persistent lesions, CD8 T cells had a distinct localization pattern (p = 0.07 in concordant set, linear model), in which CD8 T cells lined and were embedded in the epithelium in areas where dysplasia is present (Figure 4D). The immunofluorescence results did not reach significance, with the exception of CD163, when only the lesion outcome was used without taking into account the score for Module 9.

Discussion

[0243] Squamous cell carcinoma of the lung (LUSC) is the second most common form of lung cancer and arises in the epithelial layer of the bronchial airways.

It is often preceded by the development of premalignant squamous lung lesions (PMLs). The presence of persistent and/or progressive dysplastic PMLs is a marker of increased risk for LUSC (6). Currently, however, effective tools are lacking to identify PMLs with a higher risk of progression to invasive carcinoma (7). The development of predictive markers of disease progression will be important in identifying patients at increased risk of developing LUSC and in identifying exploitable biological pathways for LUSC chemoprevention. For this purpose, the profile through bronchial smears by RNA-Seq and endobronchial biopsies obtained from individuals submitted to longitudinal screening for lung cancer using computed tomography (CT) of the chest and autofluorescent bronchoscopy is described in this document. Four transcriptionally distinct groups of biopsies are identified, one marked as proliferative and associated with high-grade dysplasia.

Patients with proliferative PMLs can also be identified through gene expression measured from cells in the uninvolved upper airway epithelium. It was also found that persistent/progressive proliferative PMLs are characterized by decreased expression of genes involved in interferon signaling and in antigen processing/presentation pathways.

Consistent with these gene expression findings, progressive/persistent proliferative PMLs were found to be depleted to CD68+/CD163+ macrophages and CD8 T cells by immunofluorescence. Collectively, these data indicate the potential to identify a subset of patients with progressive/persistent LUSC who are at risk for developing invasive lung cancer, based on airway gene expression; as well as the potential to decrease the risk of progression in these patients, increasing the immune response associated with regression.

[0244] Previous studies indicate a variety of genomic alterations associated with bronchial dysplasia. Increased EGFR expression and Ki67 staining of epithelial cells is associated with increased histological severity and subsequent histological progression (6, 17).

Altered levels of TP53, CCND1, CCNE1, BAX and BCL2 proteins were associated with the occurrence of CIS or lung cancer regardless of histological grade (18). Shortening and maintenance of telomeres (19) and loss of heterozygosity in regions frequently detected in lung cancer (3p, 5q, 9p, 13q, 17p) were observed in early hyperplasia/metaplasia lesions (20-22) and increased in frequency and size in high-grade dysplasia. Genomic gains in loci containing SOX2, TP63, EGFR, MYC, CEP3 and CEP5 are also associated with the progression of high-grade dysplasia (23). Despite the numerous genomic alterations associated with the histological grade and progression of PML, a comprehensive molecular classification system for PMLs is lacking to complement the pathological classification of PMLs. The use of an unsupervised class discovery approach led to the identification of four distinct molecular subtypes of PML (Proliferative, Inflammatory, Secretory, and Normal).

[0245] The transcription patterns that differentiate PML subtypes are robust and a panel of 22 genes identified in the Discovery Cohort can be used to distinguish between the different molecular subtypes in an independent Validation Cohort. Interestingly, although a prior history of lung cancer can influence airway gene expression and about two-thirds of individuals have a prior history of lung cancer, we did not detect a significant association between a history of lung cancer and the subtype. There is a similar diversity of molecular subtypes between biopsies taken from individuals with and without a history of lung cancer. The Proliferative subtype is enriched with dysplastic PMLs from current smokers and is characterized by upregulation of metabolic pathways (OXPHOS/ETC/TCA) and cell cycle and downregulation of pathways associated with cilia. Previous work indicates increases in metabolic pathways in the airways of individuals with dysplastic lesions (13), in PMLs adjacent to the LUSC tumor (24) and in smokers at high risk of lung cancer (25), as well as increases in proliferation (via Levels of Ki67, as mentioned above) that were used as an end point in lung cancer chemoprevention (26, 27). Identifying patients with proliferative lesions is useful to enrich lung cancer chemoprevention trials with high-risk individuals or to identify patients who would benefit from more frequent lung cancer screening. The Inflammatory subtype is predominant in PMLs from ex-smokers, however, interestingly, it is not significantly enriched in dysplasia, despite the decreased expression of pathways associated with the cilia, suggesting an abnormal epithelium.

The Inflammatory subtype also shows increased expression of a gene module enriched in genes involved in inflammation and lymphocyte and leukocyte regulation (Module 8). This gene module is also elevated in Secretory lesions predominated by lesions of current smokers and which exhibit increased expression of goblet cell markers.

Interestingly, IL1B is part of this inflammation-related gene module, which is of great interest as it has recently been shown that inhibition of IL1B reduces the incidence of lung cancer (28).

[0246] Our previous work has extensively studied gene expression changes in normal-appearing airway epithelium by profiling cells obtained by smearing the main bronchus during bronchoscopy (8, 29 35, 35). As part of this work, alterations in gene expression that reflect the presence of bronchial dysplasia have been described (31). In the current study, for the first time, both bronchial smears and endobronchial biopsies were collected during the same procedure, allowing the identification of gene expression differences in normal-appearing bronchial airway smears that indicate the presence of PMLs of the Proliferative subtype.

In both the Discovery Cohort and the Validation Cohort, applying the predictor used to identify PMLs of the Proliferative subtype (based on gene expression in the PML biopsy) to gene expression data from normal-looking airway smears resulted in predictions of the Proliferative subtype that were very specific (91%) but not sensitive (31-38%). Smears classified as

Proliferatives had increased expression of cell cycle pathways and reduced expression of cilia-associated genes, suggesting that they are more similar to squamous metaplasia than to normal epithelium. Potentially, a subset of patients may have widespread airway damage that serves as a marker for the presence of this type of high-grade PML, leading to modest sensitivity but high specificity. In other cases, the area of damage that gives rise to these proliferative PMLs may be more localized and therefore potentially more difficult to detect, contributing to decreased sensitivity. These findings indicate that a therapy that targets variations along the entire airway epithelium may be needed in some individuals, while more site-specific ablation (eg, photodynamic therapy) may be more effective in certain cases. Another possibility and area of future research is that a smear of the Proliferative subtype is a predictor of incident LUSC.

[0247] Molecular profile characterization of PMLs and identification of gene coexpression modules also provide an opportunity to identify the molecular determinants of subsequent progression of PMLs. One of the nine gene coexpression modules used to define the molecular subtypes was significantly different between biopsies that progress or persist compared to biopsies that regress within the Proliferative subtype in both the DC and VC cohorts. The module contains genes whose expression is decreased in persistent/progressive biopsies that are involved in interferon signaling and in antigen processing and presentation. These variations in gene expression were correlated with a decrease in the abundance of innate and adaptive immune cells through computational prediction. By immunofluorescent staining of FFPE biopsy sections, it was confirmed that progressive/persistent proliferative lesions with low GSVA scores for Module 9 had fewer CD163+ macrophages and CD8+ T cells and CD8+ T cells had a distinct localization pattern. These lesions also contained a greater number of CD4+ T cells and it will be important in future work to assess whether these cells are regulatory T cells that promote an immunosuppressive environment.

[0248] The presence of tumor-associated macrophages with polarized phenotypes (M1 as pro-inflammatory or M2 as anti-inflammatory) was associated with the prognosis of lung cancer. The predominantly presence of M2 macrophages, marked by the expression of CD163, has been associated with poorer survival. However, in the context of pulmonary PMLs, this relationship is not well studied. The present finding that proliferative regressive PMLs have more CD163+ cells and increased expression of genes involved in IFN signaling is consistent with what was observed in PMLs that precede oral squamous cell carcinoma, where the presence of CD163+ macrophages with active signaling to IFN is associated with better results (36). Furthermore, fewer CD8+ T cells and lower expression of Class I and B2M HLA genes were observed in progressive/persistent lesions within the Proliferative subtype.

Disruptions in adequate T-cell-mediated immunosurveillance have been described in several studies that show compromised HLA Class I antigen processing and presentation, including down-regulation or loss of B2M (37, 38) and interferon signaling (39) in tumors affects the response and acquired resistance to checkpoint inhibitors. Lung tumors without an HLA-I complex had less infiltration of cytotoxic CD8+ lymphocytes, and this was also associated with lower levels of PD-L1. Furthermore, studies have also suggested negative impacts on the efficacy of checkpoint inhibitors as well as on survival in LC patients who have tumors with increased CD4+ T cells that express regulatory T markers (FOXP3, CD25) resulting in an immunosuppressive state suggested for impede recruitment and effector functions of CD8+ T cells (40,

41). Future DNA sequencing data on the PMLs profiled in this document may indicate heterozygous or homozygous loss of B2M or mutations in other genes in the antigen and interferon presentation and processing pathways; however, even in the case of acquired resistance, mutations and copy number alterations could not explain the downregulation of these pathways in all individuals, suggesting that other epigenetic alterations or signaling pathways might play a role.

In fact, epigenetic therapy, specifically DNA methyltransferase inhibitors (42), has been shown to increase the response to immune checkpoint therapy and up-regulate many of the down-regulated genes in progressive/persistent lesions within the Proliferative subtype,

including HLA class I genes (HLA-B and HLA-C), B2M, CD58,

TAP1, immunoproteasome subunits PSMB9 and PSMB8 and the transcription factor IRF9. Unraveling the mechanisms of innate and adaptive immune regulation in this subset of PMLs will be important to identify potential immunoprevention therapies.

[0249] The present data indicate that there are subtype-specific transcriptomic changes predictive of subsequent LUSC premalignant lesion progression that are the result of a lack of infiltrating immune cells in the lesion microenvironment. These data suggest that biomarkers to determine PML subtype and assess immune infiltration may be useful for detecting aggressive PMLs that require more intensive clinical management and altered genes in these PMLs may serve as candidates for pulmonary chemoprevention. These biomarkers can be measured directly in the PML tissue or, as indicated by the present data, they can be measured in a surrogate tissue, such as bronchial airway epithelium.

A benefit of biomarkers that predict the aggressive behavior of PMLs measured in a surrogate tissue is the potential that these biomarkers can also predict the behavior of PMLs not directly observed during bronchoscopy.

Materials and Methods Individual population in sample collection

[0250] Endobronchial biopsies and smears were obtained from high-risk subjects undergoing lung cancer screening at approximately 1-year intervals by white-light bronchoscopy and autofluorescence bronchoscopy and CT scan at Roswell.

Bronchoscopy included visualization of the vocal cords, trachea, main carina and visible subsegmental bronchial orifices without causing trauma to the bronchial wall. All abnormal and suspicious areas are biopsied twice and the lung anatomical location is recorded (Figure 14, Table 8). One biopsy was used for routine pathological evaluation and the other for molecular profile characterization. In addition, a smear was taken from a normal-looking area of the left or right main bronchus for research. The morphological criteria used to assess biopsies are in accordance with the guidelines of the World Health Organization (WHO) (43). Eligibility for screening includes a prior history of aerodigestive cancer and no illness at enrollment or age over 50, a current or prior history of smoking for a minimum 20 pack-year exposure, and at least one additional risk factor, including moderate chronic obstructive pulmonary disease (COPD) (defined as forced expiratory volume (FEV1) < 70%), confirmed asbestos-related lung disease, or a strong family history of lung cancer (at least 1-2 first-degree relatives). All research samples were stored in Allprotect RNA (Qiagen) and stored at -80 degrees C.

[0251] Subjects were selected who had biopsies collected at repeated sites by serial bronchoscopy; however, after RNA isolation, samples from 3 individuals had a single biopsy and 1 individual had a single smear. mRNA sequencing was performed in a Discovery Cohort (DC) of samples comprising endobronchial biopsies and smears collected between 2010 and 2012 (n = 30 subjects, n = 197 biopsies and n = 91 smears). mRNA sequencing was subsequently performed in a Validation Cohort (VC) of samples comprising endobronchial biopsies and smears collected between 2012 and 2015 (n = 20 subjects, n = 111 biopsies and n = 49 smears). Smear histology was defined by the worst biopsy histology observed at the same time point. Biopsy progression/regression was defined for each biopsy based on the histology of the biopsy and the worst histology recorded for the same lung anatomical location in the future. Histological changes between normal, hyperplasia and metaplasia were classified as "stable normal", decreases in the grade of histological dysplasia or dysplastic histology changes to normal/hyperplasia/metaplasia were classified as "regressive", the lack of future histological data was classified as "unknown" and everything else was classified as "progressive/persistent". The Institutional Review Boards at Boston University Medical Center and Roswell approved the study and all subjects who provided written informed consent.

Preparation, sequencing and data processing of the RNA-Seq library

[0252] Total RNA was extracted from endobronchial biopsies and bronchial smears using the miRNeasy™ Mini Kit or the AllPrep™ DNA/RNA/miRNA Universal Kit (Qiagen). Library sequences were prepared from total RNA samples using the Illumina TruSeq™ RNA Kit v2 and multiplexed into groups of four using the Illumina TruSeq™ Paired-End Cluster Kit.

Each sample was sequenced on the Illumina HiSeq™ 2500 to generate matched-end 100 nucleotide reads. Demultiplexing and creation of FASTQ files were performed using Illumina CASAVA™ 1.8.2 or BaseSpace.

Samples were aligned using hg19 and 2-pass STAR alignment (44). Gene and transcription level counts were calculated using RSEM (45) using Ensembl™ v74 annotation. Quality metrics were calculated by STAR and RSeQC (46). Samples in which gender annotation did not correlate with gene expression through CYorf15A (ENSG00000131002), DDX3Y (ENSG00000067048), KDM5D (ENSG00000012817), RPS4Y1 (ENSG00000129824), USP9Y (ENSG00000114374) and UTY18387 (ENSG000) were excluded 4 samples). The sample relationship within a patient was confirmed using Peddy™ software (47).

[0253] Samples with a high rate of heterozygosity (more than 3 standard deviations above the median) or samples with a low ratio to samples from the same patient (more than 3 standard deviations below the median) were removed from further analyzes (n = 11 samples, 2 smears and 9 biopsies). Samples were subsequently divided into Discovery and Validation cohorts (as described above) and by tissue type (biopsy or smear). Subsequent gene collection and filtering were conducted separately on each set as follows: first, EdgeR™ (48) was used to compute normalized data (normalized library sizes using TMM, trimmed mean M values and log2 counts per computed million) and those genes that had an interquartile range equal to zero or a sum between samples equal to or less than 1 were excluded.

Samples were excluded based on values greater than 2 standard deviations from the mean for more than one of the following criteria: 1) Pearson's mean correlation with all other samples calculated on all filtered genes, 2) the first or second principal components calculated using the filtered gene expression matrix, 3) the transcript integrity number (TIN, calculated by RSeQC). After sample filtration, gene filtration was recalculated as described above in the final set of high quality samples. The data is available in the NCBI Gene Expression Omnibus using the GSE109743 accession.

Derivation of Molecular Subtypes

[0254] Biopsies (n = 190 samples, n = 16653 genes) and smears (n = 89 samples, n = 16058 genes) on CD were used to derive the molecular subtypes. Two additional RNA-Seq datasets were used during the derivation of the molecular subtypes: the TCGA squamous cell carcinoma (LUSC) tumors (10) (n = 471 samples, n = 17887 genes) and a sample dataset tracheobronchial arteries of mice treated with n-nitrosotris-(2-chloroethyl)urea (NTCU) (n = 25 samples, n = 14897 genes).

Mice develop lesions that are histologically and molecularly comparable to human lesions that progress to LUSC and the samples represent a variety of histology (normal, mild dysplasia, moderate dysplasia,

severe dysplasia, carcinoma in situ (CIS) and LUSC tumor). The mouse data is available in the NCBI Gene Expression Omnibus using accession ID GSE111091. Sample and gene filtration from TCGA LUSC tumors and mouse tissue were processed as described elsewhere in this document.

[0255] Weighted correlation network analysis (9) (WGCNA) was used with default parameters to derive Gene Coexpression Modules through the 4 datasets described above. Residual gene expression values adjusted for RNA quality (median TIN) and batch (Illlumina flow cell) were used as input to WGCNA for the biopsy and smear datasets. For the mouse dataset, residual gene expression values adjusted for RNA quality (median TIN), mouse strain and sample type (microdissected laser capture versus whole tissue) were used as input to WGCNA.

Log2 counts per million (cpm) values were used as input to WGCNA for the LUSC tumor samples. Gene sets were created for each coexpression module for each data set and then combined to create a compendium of gene sets generated from each of the 4 data sets. For each gene defined in the compendium, the first major component (PC1) was calculated in each z-score normalized data set. For each dataset, a Pearson correlation matrix of PC1 values across all gene sets in the compendium was calculated and the thresholds were defined as follows: r > 0.85 was defined as 1 and r <= 0.85 set to 0. The four arrays were subsequently summed and the sets of genes derived from Biopsy Coexpression Modules that were correlated to another set of non-biopsy derived genes in all data sets were retained (n = 9 Modules retained). The genes defining the retained Biopsy Modules should be present in the Biopsy Module and at least one of the correlated gene sets.

[0256] The above filtration process yielded a reduced set of genes (n = 3936) that were used to define the molecular subtypes in the biopsy data. The residual gene expression values in the reduced gene pool for Discovery biopsies were used as input for consensus clustering (49). Consensus clustering was performed by setting k (number of clusters) to 10, the number of iterations to 1000, subsampling to 80%, the clustering algorithm for partitioning around mediodes, and the distance metric for Pearson correlation. The ideal value for k was 4 based on the relative variation in area under the cumulative distribution function calculated based on the consensus matrix for each k.

Molecular subtype predictor

[0257] Biopsies in CD from the filtered genes were used to derive a predictor of molecular subtype.

First, Pearson correlation metrics were determined between each gene and the Eigengene Module (PC1 for each of the 9 Modules). Genes were retained as part of a module if the correlation value was higher for the module to which it was assigned. The mean Pearson correlation of retained genes for the Eigengene Module was calculated, and the number of genes chosen from each module for the predictor was inversely proportional to this metric.

Next, the genes most highly correlated to the genes of the Eigengene Module were chosen to represent the module in the predictor. The 22 genes resulting from this analysis in the CD biopsy data were used to train a closer centroid predictor using the pamr package with a zero threshold and predict the molecular subtype in the CV biopsies. Before predicting the molecular subtype of these test sets, the training and test sets were fit in combat (50) and the z-score normalized between the combined training and test data. Using the methods described above, we derived molecular subtypes using consensus clustering among the CV biopsies and compared them to predicted subtypes.

Identification of biological processes associated with gene modules and molecular subtypes

[0258] The biological processes and pathways enriched in each of the nine modules used to discover molecular subtypes in DC were identified using EnrichR (51).

Each module was separated into genes correlated positively or negatively with the Eigengene Module, Ensembl IDs were converted to Genetic Symbols using biomaRt and the following databases were queried: GO Biological Process 2015, KEGG 2016, WikiPathways 2016, microRNA TargetScan, Fator of Transcription PPIs, TRANSFAC and JASPAR PWMs, OMIM Disease, Reactome 2016 and Biocarta 2016.

Processes/lanes with an FDR < 0.05 were considered significantly enriched. The contribution of each gene module to the molecular subtypes of biopsy in CD was assessed by testing whether the GSVA scores (14) for each module were significantly (FDR < 0.05) associated with the molecular subtypes using a linear mixed-effect model with the patient. as a random limma effect.

Identification of associations of clinical and biological phenotype with molecular subtype

[0259] Molecular subtypes in biopsies in CD were noted according to the behavior of each gene module, calculating whether the GSVA scores (14) for each module were significantly up- or down-regulated (FDR < 0.05) at a given molecular subtype versus all other samples using a linear mixed effects model with the patient as a random effect via limma. In addition, the biological pathways and transcription factors associated with each subtype were identified using GSEA (52) and mSigDB (53) gene sets using genes ranked by t-statistics for their association with each subtype. Ranked lists were created using the limma (54) and edgeR (48) packages to identify differentially expressed genes associated with subtype association.

[0260] Each linear model used voom-transformed data (55) and included the association in subtype of interest, batch and RNA quality (TIN) as covariates and patient as a random effect. Routes enriched in ranked lists (FDR < 0.05) were used to annotate molecular subtypes. FDR values for individual genes were derived from this analysis or analogous models using only normal histology/hyperplasia or dysplasia histology samples.

[0261] For biopsies in CD and VC, residual gene expression values were used to predict smoking status, LUSC tumor subtype, and relative abundance of epithelial and immune cells for each sample. Smoking (current versus previous/never) was predicted for each sample as described above (13). Smoking status was determined at each time point for each subject by averaging the prediction scores (>0 for current prediction and <0 for previous/never prediction) across all biopsies and smears collected. The LUSC tumor subtype was determined as previously described (11) through the predictive genes of the LUSC molecular subtype (12). The ESTIMATE algorithm (56) was used to infer the relative content of epithelial, stromal and immune cells.

Immune cell type-specific signatures of Bindea et al. (15) and epithelial cell type-specific signatures of Dvorak et al. (50) were used to generate GSVA scores (14) on samples for each signature. In addition, residual gene expression values calculated using log RPKM values were entered into xCell (16) to infer the relative abundances of 64 different cell types. The above categorical phenotypes, along with additional clinical variables such as biopsy histology, individual, previous history of lung cancer,

gender and biopsy progression/regression status were associated with molecular subtype using Fisher's Exact Test. Continuous variables were associated with the molecular subtype using a linear model via limma.

[0262] In order to characterize the molecular changes associated with the lesion outcome, a linear mixed effects model was used to assess the scoring differences for the GSVA Module between progressive/persistent versus regressive lesions within each molecular subtype with the patient as a random effect via limma. We estimated the differences in immune cell content (separately for xCell and Bindea et al.) between progressive/persistent versus regressive lesions in the Proliferative subtype using a linear mixed effects model that corrects for epithelial cell content ('Epithelial' in xCell and 'Normal Mucosa' in Bindea et al.) and the patient as a random effect. We focused on cell types that were significantly different (FDR < 0.05) between progressive/persistent versus regressive lesions in the Proliferative subtype in both the Discovery Cohort and the Validation Cohort.

Relationship between biopsies and smears

[0263] It was desired to quantify the predictive performance of the smear in relation to the presence of a subtype biopsy

Proliferative. A subset of 22-gene molecular subtype predictors was used to predict the presence or absence of the Proliferative subtype in smears and biopsies in CD and VC. Specifically, 8 genes (out of 22) that corresponded to Modules 4 to 7 (significantly up- or down-regulated in the Proliferative subtype) were used to classify the samples as proliferative or not using the same methodology described above for the molecular subtype predictor. Sensitivity and specificity performance metrics were calculated based on the ability of a Proliferative subtype prediction in smears in CD or VC to indicate the presence of at least one Proliferative subtype biopsy.

In order to better understand the Proliferative subtype predictions in the smears, the behavior of the modules defining the Proliferative subtype in the CD biopsies (based on the above methods) was analyzed in the CD and VC smears.

[0264] Immunofluorescent staining and quantification

[0265] Standard formalin fixation and incorporation techniques were employed at Roswell, where 5-micron sections were cut from the FFPE samples used for routine pathological evaluation at Roswell (Table 7). Prior to staining, samples were removed from the wax with xylene and rehydrated using a graded series of ethanol solutions. RA or citrate buffer was used for antigen retrieval, tissue was incubated with primary antibodies overnight at 4°C and hybridized with secondary antibodies with fluorescent conjugates (Invitrogen Alexa Fluor 488, 594, 647) for 1 hour at room temperature .

Immunostaining was performed using the primary antibodies listed in Table 9. Imaging was performed using an Aperio Slide Scanner for scoring and a Carl Zeiss Axio (20x and 40x objectives) and a Carl Zeiss LSM 710 NLO confocal microscope to capture additional images. Digital slides were analyzed with the Definiens Tissue Studio (Definiens Inc.) for enumeration of immunofluorescence staining. Immunofluorescence enumeration scored each stain, including DAPI positive cells. Counting was performed on different regions (independent tissue areas) present on a slide (1-5 regions/biopsy) for each biopsy. For each region, the percentage of cells staining positive for a particular protein was calculated by dividing the number of cells staining positive by the total number of cells positive for DAPI. A binomial mixed effects model via the lme4 R package was used to assess the differences in the percentages of cells with positive staining for a particular protein in each region between progressive/persistent versus regressive biopsies using the total cells stained in each region as weights and adjusting to the blade number as a random effect. The models were used on Proliferative subtype samples and on Proliferative subtype samples where the biopsy result (progressive/persistent versus regressive) agreed with the GSVA score from Module 9 (scores less than 0 are associated with progression/persistence and higher scores on the that 0 are associated with the regression). Each region was also qualitatively assessed as positive or negative by having a distinct CD8 T cell localization pattern, in which the cells coated and were incorporated into the epithelium.

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Table 1. Demographic and clinical note on individuals in both Discovery and Validation cohorts. Statistical tests between Discovery and Validation cohorts were performed using Fisher's exact test for categorical variables and Student's t test for continuous variables.

Percentages are reported for categorical variables and mean and standard deviations are reported for continuous variables Discovery Cohort Validation (n=20 Variable (n=30 individuals) Individual p-value) Mean # Biopsies/Individual 6.6 (5 .7) 5.25 (2.9) 0.3 Average # Bronchoscopy/ Individual 2.8 (1.5) 2.4 (0.8) 0.27 Average Time Between Bronchoscopy (Days) 368.2 ( 201.4) 360.1 (212.5) 0.87 Men 15/30 (50) 12/20 (60) 0.57 White 27/30 (90) 17/20 (85) 0.67 Age (in Baseline Clinical Visit) 58.8 (7.6) 58.7 (8.3) 0.97 Ex-smoker (in the Line Clinical Visit of 29/30 (96.7) 19/20 (95) 1 Base) Previous History of Lung Cancer 21/30 (70) 12/20 (60) 0.55 COPD (FEV1/FVC <= 0.7, at the Clinical Visit of 17/27 (63.0) 8/18 (44.4) 0.24 Baseline) GOLD 1 (FEV1 % > 80) 2/27 (7.4) 2/18 (11.1) 1 GOLD 2 (FEV1 % < 80 and > 50) 12/ 27 (44.4) 5/18 (27.8) 0.35 GOLD 3 (FEV1 % < 50 and > 30) 3/27 (11.1) 1/18 (5.6) 0.64 Occupational Asbestos 13 /30 (43.3) 9/20 (45) 1 Occupational Work of High Risk 14/30 (46.7) 12/20 (60) 0.4

Discovery Cohort Validation Cohort Variable P-value (n=30) (n=20)

Mean # Biopsies/Individual 6.6 (5.7) 5.25 (2.9) 0.3

Mean # Bronchoscopies/ Individual 3.1 (1.6) 2.5 (0.7) 0.08

Mean Time Between Bronchoscopy (Days) 348.6 (197.5) 366.8 (208.3) 0.69

Men 15/30 (50) 12/20 (60) 0.81

Whites 27/30 (90) 17/20 (85) 1

Age (at the Line Clinic Visit of 58.8 (7.6) 58.7 (8.3) 0.97 Base)

Ex-smoker (at the Clinical Visit of Line 29/30 (96.7) 19/20 (95) 1 Base)

Pack-years 49.8 (22.1) 41.3 (20.7) 0.17

Previous History of Lung Cancer 21/30 (70) 12/20 (60) 0.82

LUSC 5/30 (16.7) 5/20 (25) 0.73

Other 16/30 (53.3) 7/20 (35) 0.6

COPD (FEV1/FVC <= 0.7, at Clinical Visit 17/27 (63.0) 8/18 (44.4) 0.61 Baseline)

GOLD 1 (FEV1 % > 80) 2/27 (7.4) 2/18 (11.1) 1

GOLD 2 (FEV1 % < 80 and > 50) 12/27 (44.4) 5/18 (27.8) 0.56

GOLD 3 (FEV1 % < 50 and > 30) 3/27 (11.1) 1/18 (5.6) 1

Occupational Asbestos 13/30 (43.3) 9/20 (45) 1

High Risk Occupational Work 14/30 (46.7) 12/20 (60) 0.62

Table 2. Clinical annotation on samples in both Discovery and Validation cohorts.

Statistical tests between Discovery and Validation cohorts on biopsies or smears were performed using Fisher's Exact Test and percentages are reported Variable Discovery Cohort Validation Cohort P-value

Sample Type Smear Biopsies Smear Biopsies Smear Biopsies

Histology 0.05 0.42

Normal 38/190 (20) 6/89 (6.7) 23/105 (21.9) 0/48 (0)

Hyperplasia 30/190 (15.8) 11/89 (12.4) 31/105 (29.5) 9/48 (18.8)

Metaplasia 46/190 (24.2) 15/89 (16.9) 14/105 (13.3) 9/48 (18.8)

Mild Dysplasia 21/190 (11.1) 9/89 (10.1) 13/105 (12.4) 6/48 (12.5)

Moderate Dysplasia 38/190 (20) 130/89 (33.7) 20/105 (19.0) 8/48 (37.5)

Severe Dysplasia 12/190 (6.3) 17/89 (19.1) 4/105 (3.8) 8/48 (12.5)

CIS 1/190 (0.5) 0/89 (0) 0/105 (0) 0/48 (0)

Tumor 0/190 (0) 1/89 (1.1) 0/10S (0) 0/48 (0)

Histology 4/190 (2.1) 0/89 (0) 0/10S (0) 0/48 (0) Unknown

Current Smoker 122/190 (64.3) 50/89 (56.2) 53/105 (50.5) 27/48 (56.3) 0.03 1 (Genomic Forecast)

Progression Status 0.39

Normal/Stable 47/190 (24.7) 35/105 (33.3)

Progressive/ 44/190 (23.2) 20/105 (19.0) Persistent

Regressive 30/190 (15.8) 18/105 (17.1)

Unknown 69/190 (36.3) 32/105 (30.5)

Variable Discovery Cohort Validation Cohort p-Value

Sample Type Smear Biopsies Smear Biopsies Smear Biopsies

Histology 0.05 0.42

Normal 38/190 (20) 6/89 (6.7) 23/105 (21.9) 0/48 (0)

30/190 (15.8) 11/89 Hyperplasia 31/105 (29.5) 9/48 (18.8) (12.4)

46/190 (24.2) 15/89 Metaplasia 14/105 (13.3) 9/48 (18.8) (16.9)

Mild Dysplasia 21/190 (11.1) 9/89 (10.1) 13/105 (12.4) 6/48 (12.5)

38/190 (20) 130/89 Moderate Dysplasia 20/105 (19.0) 8/48 (37.5) (33.7)

Severe Dysplasia 12/190 (6.3) 17/89 (19.1) 4/105 (3.8) 8/48 (12.5)

CIS 1/190 (0.5) 0/89 (0) 0/105 (0) 0/48 (0)

Tumor 0/190 (0) 1/89 (1.1) 0/10S (0) 0/48 (0)

Histology 4/190 (2.1) 0/10S (0) 0/48 (0) Unknown 0/89 (0)

Current Smoker 119/190 (62.5) 38/105 (36.2) 20/48 (41.7) 1.80E-05 0.47 (Genomic Forecast) 44/89 (49.4)

Progression Status 0.39

Normal/Stable 47/190 (24.7) 35/105 (33.3) Progressive/ 44/190 (23.2) 20/105 (19.0) Persistent Regressive 30/190 (15.8) 18/105 (17.1) Unknown 69/190 (36.3) 32/105 (30.5) Table 3. Summary of molecular subtype characteristics in the Discovery cohort. For each molecular subtype, significant associations are reported with each of the 9 gene modules, clinical features, canonical cell type epithelial and white blood cell gene markers, pathways

PROLIFERATIVE Modules positively 4, 5, 7 regulated Modules negative 6 regulated Clinical Characteristics Current smoker (88%), dysplastic biopsies (63%) Characteristics Subtypes of SCC – Basal and Classic; TUB5A1, SCG8141 Biological down-regulated; KRT5, KI67 Positively Regulated Cell Cycle Pathways: BUB1B/1/3, CHEK1/2, CDK1/2/4/6, E2F1/3/2/4, MCM4/3/5/6/7, TP53, RB1 Repair DNA: TP53, PARP1, RAD51, BRCA2, FANCA/D2/G/E/M/C, XRCC5/6, ERCC6 Oxidative phosphorylation and electron transport chain: ATP synthases, NADH ubiquinone oxidoreductases, cytochrome C oxidases TFs E2

INFLAMMATORY

Modules positively 1, 2, 7, 8 regulated Modules negatively regulated 4, 5, 6 regulated Clinical Characteristics Former smoker (59%), non-dysplastic biopsies (68%) Characteristics Subtypes of LUSC – Secretor: TUB1A1, MUC5AC negatively regulated Pathways Extracellular matrix , focal adhesion and integrin pathways: collagen, integrin and laminin genes Cytokine/chemokine: CCL2/14/19/21/28, CVCX12/14/5, CCR1/2/3/4/5, IL18, IL11RA, IL18RB , IL3RA, EGF, IL15, CX3CR1, TGFB1/B2/B3, KIT Down regulation of oxidative phosphorylation, respiratory electron transport, cell cycle TFs SRF

SECRETOR Positively 6, 8 regulated modules Negatively regulated 1, 2, 5, 7 modules Clinical Characteristics Current smoker (63%), non-dysplastic biopsies (68%) Characteristics Subtypes of SCC – Secretor: CD45, MUC5AC, TUB2A1 Biological positively regulated, KI67 , KR15 down-regulated pathways Extracellular matrix down-regulation, focal adhesion and TFs integrin pathways E2F down-regulation

NORMAL Modules positively 1, 6 regulated Modules negative 8, 9 regulated

Clinical Features Former smoker (65%), non-dysplastic biopsies (75%) Features CD45, MUC5AC, down-regulated KI67; SCGB1A1, KRT5, Biological TUB1A1 up-regulated pathways Central extracellular matrix genes: collagen and laminin genes, WISP1/2 Innate and adaptive immunity down-regulation: HLA genes, IRF1/4/7/8, TLR2/4/6/6/ 8/10, IK8KB TFs Negative regulation of PEA3, IRF, NFkB

PROLIFERATIVE Modules positively 4, 5, 7 regulated Modules negative 6 regulated Clinical Characteristics Current smoker (88%), dysplastic biopsies (63%) Characteristics LUSC Subtypes – Basal and Classic; TUB5A1, SCG8141 Biological down-regulated; KRT5, KI67 Positively Regulated Cell Cycle Pathways: BUB1B/1/3, CHEK1/2, CDK1/2/4/6, E2F1/3/2/4, MCM4/3/5/6/7, TP53, RB1 Repair DNA: TP53, PARP1, RAD51, BRCA2, FANCA/D2/G/E/M/C, XRCC5/6, ERCC6 Oxidative phosphorylation and electron transport chain: ATP synthases, NADH ubiquinone oxidoreductases, cytochrome C oxidases Transcription Factors E2F

INFLAMMATORY Modules positively 1, 2, 7, 8 regulated Modules negatively regulated 4, 5, 6 regulated Clinical Characteristics Previous smoker (59%), non-dysplastic biopsies (68%)

Characteristics SCC Subtypes – Secretor: TUB1A1, MUC5AC negatively regulated Biological Pathways Extracellular matrix, focal adhesion and integrin pathways: collagen, integrin and laminin genes Cytokine/chemokine: CLL2/14/19/21/28, CCR1/2/3 /4/5, IL18, IL11RA, IL17RB, IL3RA, EGF, IL15, CX3CR1, TGFB1/B2/B3, KIT Down regulation of oxidative phosphorylation, respiratory electron transport, cell cycle Transcription Factors SRF

SECRETOR Positively 6, 8 regulated modules Negatively regulated 1, 2, 5, 7 modules Clinical Characteristics Current smoker (77%), non-dysplastic biopsies (66%) Characteristics LUSC subtypes – Secretor: CD45, MUC5AC, TUB1A1 Biological positively regulated, KI67 , KR15 down-regulated Pathways Extracellular matrix down-regulation, focal adhesion, and integrin pathways Transcription Factors E2F down-regulation NORMAL-LIKE Up-regulated modules 1, 6 down-regulated Modules down-regulated 8, 9-regulated Clinical Features Former smoker (65%), non-biopsies dysplastic (75%) Characteristics CD45, MUC5AC, KI67 down-regulated; SCGB1A1, KRT5, Biological TUB1A3 up-regulated pathways Central extracellular matrix genes: collagen and laminin genes, WISP1/2

Down Regulation of Innate and Adaptive Immunity: HLA Genes, IRF1/4/7/8, TLR2/4/6/8/10, IK8KB Transcription Factors Down Regulation of PEA3, IRF, NFkB EXAMPLE 2: Supplemental Material for Example 1 Materials and Methods N-nitrosotris-(2-chloroethyl)urea (NTCU) for mouse sample collection and library preparation

[0266] We previously collected and stored RNA from 40 fresh frozen whole lung sections (bunches) and laser microdissected tissue (LCM) isolated with an Acrutus Pixcell™ II instrument from NTCU-treated SWR/J and A/J mice. Mice were treated topically with 15 or 25 µmol of NTCU (25 µl of NTCU at 40 mM for 15 or 25 weeks) as part of a study performed according to the protocol approved by IACUC at the RPCC. Samples include examples of: normal (SWR/J n = 3 LCM & 3 curls and A/J n = 2 LCM and 1 curls), metaplasia/mild dysplasia (SWR/J n = 5 LCM & 2 curls), moderate dysplasia (SWR/J n = 7 LCM and 4 bunches and A/J n = 2 LCM and 1 bunches) and severe dysplasia (SWR/J n = 3 LCM and 2 bunches) and carcinoma in situ/LUSC (A/J n = 2 LCM and 2 curls). Samples were extracted using the Qiagen mi-RNAeasy kit according to the manufacturer's protocol. Sequencing libraries will be prepared from total RNA samples using the Illumina TruSeq v2 sample preparation kit. Each sample was sequenced at five per row on the Illumina HiSeq 2500 to generate 50 single-ended nucleotide reads.

Histological classification of RNA from sequenced NTCU mouse samples (n = collected / n = QC passed after sequencing) Dysplasia Tumor Dysplasia Type Lineage Moderate Normal Dysplasia/ CIS/SCC Total mouse sample Mild Severe Severe A/J LCM 2/2 - 2/2 - 2/1 6/5 A/J 1/1 - 1/1 - 2/1 4/3 SWR/J LCM Curls 4/1 5/3 7/3 3/1 19/8 SWR/J 11/9 3/3 2/2 4/3 2/1 Total Curls 40/25 Average RIN Values 4.0 3.4 3.8 (0.5) 3.3 (0.6) 2.55 (0 .1) (SD) (1.8) (1.2) Mouse NTCU Data Processing

[0267] Demultiplexing and creating FASTQ files were performed using Illumina CASAVA 1.8.2.

Trimmomatic was used to trim adapter sequences as well as to trim low quality reads using the following parameters: ILLUMINACLIP: TruSeq3-SE.fa: 2: 30: 10, LEADING: 20, TRAILING: 20, SLIDINGWINDOW: 4:20, and MINLEN:

20. After cutting, more than 99% of readings were retained on all samples. Samples were subsequently aligned using STAR alignment (44) mm9 and 2 passes. Gene and transcription level counts were calculated using RSEM (45) using Ensembl annotation. Quality metrics were calculated by STAR and RSeQC (46).

Initially, 15 samples were removed based on the percentage of uniquely aligned readings (compared to total readings) of less than 15%. Subsequent gene sampling and filtering were conducted separately on each set as follows: first, EdgeR (48) was used to compute normalized data (normalized library sizes using TMM, trimmed mean M values and computed log2 counts per million) and were genes that had an interquartile range of zero or a sum in the samples equal to or less than 1 were excluded. The samples were excluded based on values greater than 2 standard deviations from the mean for 1) Pearson's mean correlation with all others samples calculated on all filtered genes, 2) first or second principal components calculated using the filtered gene expression matrix, 3) transcript integrity number (TIN, calculated by RSeQC). After sample filtration, gene filtration was recalculated as described above in the final set of high quality samples. The data is available in the NCBI Gene Expression Omnibus using the GSE111091 access.

Immunofluorescence Quantification of Cell Type and Proliferative Markers

[0268] Basal and hair cell type markers (KRT5 and TUB1A1) and proliferative marker (KI67) were manually enumerated for the entire epithelium in a biopsy in reference to DAPI staining, with a minimum of 500 cells counted per biopsy . Counting was performed on different regions (independent tissue areas) present on a slide (1-4 regions/biopsy) for each biopsy. A percentage of positively stained cells was calculated for each marker in each enumerated region. A binomial mixed effects model through the lme4 R package was used to assess differences in the percentages of cells with positive staining for a given protein in each region between the molecular subtypes using the total cells stained in each region as weights and adjusting for the patient as an effect.

TCGA SCC Tumor Data Processing

[0269] The Log2 transcript per million data in 20,500 genes from 476 LUSC tumors was obtained from Campbell (10) et al.

Genes that had an interquartile range of zero or a sum between samples equal to or less than 1 were excluded. Samples were excluded based on values greater than 2 standard deviations from the mean for more than one of the following criteria: 1 ) Pearson's mean correlation with all other samples calculated on all filtered genes,

2) first or second principal components calculated using filtered gene expression matrix, 3) transcript integrity number (TIN, calculated by RSeQC). After sample filtration, gene filtration was recalculated as described above (n = 17,887 genes) in the final set of high quality samples (n = 471 tumors).

[0270] Table 5 describes the pathways enriched in the Genetic Modules.

Table 5. Enriched results (FDR < 0.05) for selected pathways associated with each gene module FDR for Number of Number of Associated Biological Pathways and difference between Key Genes Module Genes Gene Modules molecular subtypes Collagens, Extracellular Matrix / Adhesion 1 514 Laminins, 2.70E-36 Cell TGFb Processing and Splicing of 2,939 RBMs & SRSF 7.20E-05 mRNA Transcriptional Regulation in Response to Stimuli - (AP- 3 20 1) JUN & FOS 1.90E-01 Immediate / Early Response Genes COXs & 4 64 OXPHOS / ETC / TCA 3.30E-07 NDUFs PCNA, Cell Cycle / Replication TOP2A, CDC, DNA 5 209 2.00E-31 / DNA Repair AURK, RAD,

XRCC

Organization and assembly 6 1295 FOXJ1, DYNC 6.60E-57 ciliary

Ribosomal Proteins / 7 180 RPLs & RPSs 1.90E-13 Translation

CD8A, CD86, Immune Activation and GATA Response, STAT, 8 603 Inflammatory (3.30E-07 IL1B regulation, leukocyte/lymphocyte) CD163, CD68

Signaling to Interferon and SP100, 9 112 Processing and Presentation 1,30E-02 HLAs, Antigen STAT1

Table 6. Molecular subtype associations with clinical and biological characteristics within the Discovery Cohort (DC) and the Validation Cohort (VC). Statistical tests in the Discovery and Validation cohorts were performed using the

Fisher's exact test

Fisher's Exact Test for Molecular Subtype V.

Variable

Variable P-value for DC P-value for VC

Genomic smoking status 1.00E-07 9.64E-03

Individual 9.66E-05 5.87E-03

Individual/Time 6.96E-04 1.40E-02

Histology 6.75E-03 9.99E-08

Location 2.57E-02 6.69E-01

Individual/Location 6.01E-02 1.95E-01

Exposure to Asbestos 1.23E-01 7.47E-02

History of Lung Cancer 1.32E-01 9.92E-01

Progression State 1.60E-01 1.67E-05

High Risk Work 4,31E-01 8,30E-01

Gender 5.62E-01 8.90E-01

Tumor Subtype LUSC 9.99E-08 1.80E-06

COPD 1.62E-01 9.38E-03 Variable P value for DC P value for VC Genomic status Smoker 2.71E-09 2.72E-04 Individual 9.66E-05 5.87E-03 Individual/Time 6.96E -04 1.40E-02 Histology 6.75E-03 9.99E-08 Location 2.57E-02 6.69E-01 Individual/Location 6.01E-02 1.95E-01 Exposure to Asbestos 1.23E-01 7.47E-02 Lung Cancer History 1.32E-01 9.92E-01 Progression Status 1.60E-01 1.67E-05 High-Risk Work 4.31E-01 8.30E-01 Gender 5, 62E-01 8.90E-01 Tumor Subtype LUSC 9.99E-08 1.80E-06 COPD Status 1.62E-01 9.38E-03 Table 7. Statistical Associations between Progression/Persistence versus Regression within Each Subtype Molecular and Cohort (DC and VC) for each gene module.

P values below 0.05 are reported. ns = not significant and N/A = insufficient samples in each group to conduct the analysis. For the molecular subtype, N = normal, S = secretory, I = inflammatory and P = proliferative Molecular subtype NNSSIIPP Cohort DC VC DC VC DC VC DC VC Number of Progressive/Persistent Lesions 5 1 17 7 7 5 15 7 Number of Regressive Lesions 3 3 8 1 4 1 15 13 Module Number 1 ns N/A ns N/A ns N/A ns ns

2 ns N/A ns N/A ns N/A ns ns

3 ns N/A ns N/A ns N/A 0.047 ns

4 0.026 N/A ns N/A ns N/A ns ns

5 ns N/A ns N/A ns N/A ns ns

6 ns N/A ns N/A ns N/A ns ns

7 ns N/A ns N/A ns N/A ns ns

8 0.027 N/A ns N/A 0.005 N/A ns ns

9 ns N/A ns N/A ns N/A 0.0017 0.03

Molecular Subtype N N S S I I P P

Cohort DC VC DC VC DC VC DC VC

Number of Progressive/Persistent Lesions 5 1 17 7 7 5 15 7

Number of Regressive Injuries 3 3 8 1 4 1 15 13

Module Number

1 ns N/A ns N/A ns N/A ns ns

2 ns N/A ns N/A ns N/A ns ns

3 ns N/A ns N/A ns N/A 0.047 ns

4 0.026 N/A ns N/A ns N/A ns ns

5 ns N/A ns N/A ns N/A ns ns

6 ns N/A ns N/A ns N/A ns ns

7 ns N/A ns N/A ns N/A ns ns

8 0.027 N/A ns N/A 0.005 N/A ns ns

9 ns N/A ns N/A ns N/A 0.0017 0.03

Table 8. Lung sites where endobronchial biopsies were obtained.

The location code, name and description are reported for each location.

ID Name Description

096 VC True vocal cords, neck

051 Oral Oral floor

007 EPIG Epiglottis

005 ART Arytenoids

008 FVC False vocal cords

095 TR Trachea

050 MC Main Carina, Carina NOS

086 RMB Right main bronchus, incl.

Right secondary carina

091 RUL Upper right lobe

093 RULO Right upper lobe hole or opening

094 RULS Upper right lobe stump

092 RULB Right upper lobe bronchus

087 RML Middle right lobe

089 RMLO Orifice or opening of the right median lobe

090 RMLS Right midlobe stump

088 RMLB Right median lobe bronchus

082 RLL Lower right lobe

084 RLLO Right lower lobe orifice

085 RLLS Right lower lobe stump

083 RLLB Right lower lobe bronchus

006 BI Intermediate Bronchus

052 RB1 Apical segment RUL (AS)

060 RB2 Posterior segment RUL (PS)

063 RB3 Previous segment RUL (ANTS)

053 RB1/2 Carina RUL between RB1 and RB2

054 RB1/3 Carina RUL between RB1 and RB3

061 RB2/3 Carina RUL between RB2 and RB3

059 RB1A/B Carina RUL AS between RB1 A and B

062 RB2A/B Carina RUL PS between RB2 A and B

064 RB3A/B Carina RUL ANTS between RB3 A and B

065 RB4 RML side segment (LS)

068 RB5 RML medial segment (MS)

066 RB4/5 Carina RML LS between RB4 and RB5

067 RB4A/B Carina RML LS between RB4 A and B

069 RB5A/B Carina RML MS between RB5 A and B

070 RB6 Upper Basal RLL Segment (SBS)

071 RB6A/B Carina RLL SBS between RB6A and B

072 RB6A/C Carina RLL SBS between RB6A and C

073 RB6B/C Carina RLL SBS between RB6B and C

074 RB7 RLL Medial Basal Segment (MBS)

075 RB7A/B Carina RLL MBS between RB7A and B

076 RB8 RLL Previous Basal Segment (ABS)

077 RB8/9 Carina RLL ABS between RB8 and RB9

078 RB8A/B Carina RLL ABS between RB8A and B

079 RB9 Basal Lateral RLL Segment (LBS)

080 RB9/10 Carina RLL LBS between RB9 and RB10

081 RB9A/B Carina RLL LBS between RB9A and B

055 RB10 Basal Posterior RLL Segment (PBS)

056 RB10A/B Carina RLL PBS between RB10A and B

057 RB10A/C Carina RLL PBS between RB10A and C

058 RB10B/C Carina RLL PBS between RB10B and C

001 666 Location has been surgically changed or removed

002 777 Abstracter needs clinical help to code

003 888 Location code is unknown, unreadable

004 999 Location code is blank, not annotated

043 LMB Left main bronchus, incl.

left secondary carina

044 LMBD Left Main Bronchus, Distal

046 LUL Upper left lobe

048 LULO Orifice or opening of the upper left lobe

049 LULS Left upper lobe stump

035 LGL Tongue

037 LGLO Orifice or lingular opening

038 LGLS Tongue stump

047 LULB Bronchus of the upper left lobe

045 LUDB Bronchus of the upper left division

036 LGLDB Bronchi of the lingular division, lingular bronchus

039 LLL Lower Left Wolf

041 LLLO Orifice or opening of the left lower lobe

042 LLLS Left lower lobe stump

040 LLLB Bronchus of the left lower lobe

009 LB1+2 LUL Apical-Posterior Segment (APS)

018 LB3 LUL Segment Previous

011 LB1/2 Carina LUL APS between LB1 and LB2

010 LB1+2/3 Carina LUL APS between LB1+2 and LB3

016 LB2A/C Carina LUL APS between LB2 A and C

017 LB2B/C Carina LUL APS between LB2B and C

019 LB3A/B Carina LUL ANTS between LB3A and B

020 LB4 Upper LUL lingular segment (SLS)

023 LB5 Inferior LUL lingular segment (ILS)

021 LB4/5 Carina LUL SLS between LB4 and LB5

022 LB4A/B Carina LUL SLS between LB4A and B

024 LB5A/B Carina LUL ILS between LB5A and B

025 LB6 Upper LLL Segment (SS)

026 LB6A/B Carina LLL SS between LB6A and B

027 LB6A/C Carina LLL SS between LB6A and C

028 LB6B/C Carina LLL SS between LB6B and C

029 LB8 LLL Segment Anteromedial Basal (AMBS)

030 LB8/9 Carina LLL AMBS between LB8 and LB9

031 LB8A/B Carina LLL AMBS between LB8A and B

032 LB9 LLL Lateral Basal Segment (LBS)

033 LB9/10 Carina LLL LBS between LB9 and LB10

034 LB9A/B Carina LLL LBS between LB9A and B

012 LB10 Basal Posterior LLL Segment (PBS)

013 LB10A/B Carina LLL PBS between LB10A and B

014 LB10A/C Carina LLL PBS between LB10A and C

015 LB10B/C Carina LLL PBS between LB10B and C

Table 9. Antibodies used in immunofluorescence studies

Immune Cell Type Markers

Antibody Company Catalog Dilution Species Antigen Recovery

CD68 Dako m0876 1-250 AR6 mouse

CD163 Cell Mark 163m-16 1-100 AR9 mouse CD4 Thermo Fisher ms1528S 1-100 AR9 mouse CD8 Dako M7103 1-100 AR9 mouse Proliferation Markers and Epithelial Cell Type Ac-α-Tub Sigma T6793 1-100 Citrate Mouse KRT5 BioLegend 905-901 1-100 Chicken Citrate KI67 Abcam ab16667 1-100 Rabbit Citrate Table 10. Genomic status of smoking over time by individual

[0271] Each individual's smoking status at each time point was calculated based on a previously published smoking-associated gene signature (see methods for details). The lines indicate smoking status at all sample times for each patient.

The → symbol indicates variations in smoking status over time. There is no statistical difference between the distribution of individuals in the smoking categories between the Discovery and Validation cohorts by a bilateral Fisher's exact test (p = 0.90). The source data is provided as a source data file.

Discovery Cohort Validation Cohort Genomic smoker status over time Number of individuals Number of individuals Current 9 9 Ex-smoker 10 5 Current → ex-smoker 7 4 Ex-smoker → current 3 2

Current → former smoker → current 1 0 Table 12. Molecular subtype associations with prior history of lung cancer: Past history of lung cancer (LC) was categorized as follows: no history (No history of LC), one prior history of LC that includes a squamous cell carcinoma of the lung (History of LC - LUSC) and a prior history of LC that does not include a squamous cell carcinoma of the lung (History of LC - Others). Statistical tests in the Discovery and Validation cohorts were performed using Fisher's bilateral exact tests.

Biopsies from the Discovery Cohort Biopsies from the Validation Cohort (n=190) (n=105) No History History No History History P- P- Variable LC - history of LC - history of LC - of LC - Value Value of LC LUSC Others from LC LUSC Others Proliferative molecular subtype 14 5 33 12 9 7 Inflammatory 10 6 21 12 4 14 Secretor 26 8 27 14 13 7 Normal 9 3 28 p=0.19 6 1 6 p=0.10

Claims (41)

1. Method of treating bronchial premalignant lesions characterized by comprising: administering at least one of: i. either a bronchoscopy-based procedure to examine the central airway or a chest CT scan; ii. at least every 6 months, one of a bronchoscopy-based procedure to examine the central airway and a chest CT scan; and/or iii. at least one antiproliferative drug; to an individual determined to have at least one of: an increased expression level of at least one module 5 gene compared to a reference level of non-proliferative lesion; and a reduced expression level of at least one module 6 gene compared to a reference level of non-proliferative lesion. Method according to claim 1, characterized in that at least one gene from module 5 is selected from the group consisting of: RACGAP1 and TPX2; and at least one of the module 6 gene is selected from the group consisting of: NEK11 and IFT88. A method according to any one of claims 1 to 2, characterized in that the subject is further determined to have an increased expression level of at least one module 7 or module 4 gene. Method according to claim 3, characterized in that at least one of the module 7 or module 4 gene is selected from the group consisting of: COX6A1; COX7A2; RPL26; and RPL23. Method according to any one of claims 1 to 4, characterized in that the expression level of each of the genes in Table 15 is determined. Method according to any one of claims 1 to 5, characterized in that at least one of the antiproliferative drug is selected from the group consisting of: acetylcholine receptor antagonists; acetylcholinesterase inhibitors; adenosine receptor antagonists; adrenergic receptor antagonists; AKT inhibitors; angiotensin receptor antagonists; apoptosis stimulants; Aurora kinase inhibitors; CDK inhibitors; cyclooxygenase inhibitors; inhibitors of cytokine production; dehydrogenase inhibitors; DNA protein kinase inhibitors; focal adhesion inhibitors; dopamine receptor antagonists; EGFR inhibitors; ERK1 and ERK2 phosphorylation inhibitors; estrogen receptor agonists; EZH2 inhibitors; FLT3 inhibitors; glucocorticoid receptor agonists; glutamate receptor antagonists; HDAC inhibitors; histamine receptor antagonists; histone lysine methyltransferase inhibitors; HSP inhibitors; IKK inhibitors; ion channel antagonists; JAK inhibitors; JNK inhibitors; KIT inhibitors; leucine-rich repeat kinase inhibitors; MDM inhibitors; mediator release inhibitors; MEK inhibitors; MTOR inhibitors; monoamine oxidase inhibitors; NFB pathway inhibitors; nucleophosmin inhibitors; PARP inhibitors; PPAR receptor agonists; PI3K inhibitors; tyrosine kinase inhibitors; phosphodiesterase inhibitors; protein kinase inhibitors; RAF inhibitors; RNA polymerase inhibitors; topoisomerase inhibitors; RNA synthesis inhibitors; SIRT inhibitors; sodium channel blockers; VEGFR inhibitors; and vitamin D receptor agonists. Method according to any one of claims 1 to 6, characterized in that the anti-proliferative drug is administered as an inhaled formulation or topical formulation. Method according to any one of claims 1 to 7, characterized in that the antiproliferative drug is administered during a procedure based on bronchoscopy. A method according to any one of claims 1 to 8, characterized in that the anti-proliferative drug is administered systemically. Method according to any one of claims 1 to 9, characterized in that the antiproliferative drug is administered during a procedure based on bronchoscopy and systemically. A method according to any one of claims 1 to 10, characterized in that the subject is further determined to have a reduced expression level of at least one module 9 gene compared to a reference level of non-proliferative lesion and/or an increased expression level of at least one module 10 gene compared to a reference level of non-proliferative lesion. A method according to claim 11, characterized in that the subject determined to have a reduced expression level of at least one module 9 gene and/or an increased expression level of at least one module 10 gene is administered with at least one of: i. either a bronchoscopy-based procedure to examine the central airway in which lesions are biopsied to remove abnormal tissue, and a CT scan of the chest; ii. at least every 6 months, one of a bronchoscopy-based procedure to examine the central airway in which lesions undergo biopsy to remove abnormal tissue and a chest CT scan; and/or iii. at least one immunostimulating drug. 13. Method of treating bronchial premalignant lesions characterized by comprising: administering at least one of: i. either a bronchoscopy-based procedure to examine the central airway in which lesions are biopsied to remove abnormal tissue, and a CT scan of the chest; ii. at least every 6 months, one of a bronchoscopy-based procedure to examine the central airway in which lesions undergo biopsy to remove abnormal tissue and a chest CT scan; and/or iii. at least one immunostimulating drug; to an individual determined to have a reduced expression level of at least one module 9 gene compared to a non-proliferative lesion reference level and/or an increased expression level of at least one module 10 gene compared to a level of reference of non-proliferative lesion. Method according to any one of claims 11 to 13, characterized in that the module 9 gene is selected from the group consisting of: EPSTI1; UBE2L6; B2M and TAP1. A method according to any one of claims 11 to 14, characterized in that at least one of the module 9 gene is selected from Table 16. 16. Method according to any one of claims 11 to 15, characterized in that the module 10 gene is selected from the group consisting of: CACNB3 and MAPK10. A method according to any one of claims 11 to 16, characterized in that at least one of the immunostimulating drug is selected from the group consisting of: immune checkpoint inhibitors (e.g. inhibitors against PD-1, PD -L1, CTLA4 and LAG3); drugs that stimulate interferon signaling (eg, antiviral drugs that improve interferon signaling); DNA synthesis inhibitors; IMDH inhibitors; CDK inhibitors; ribonucleotide reductase inhibitors; dihydrofolate reductase inhibitors; topoisomerase inhibitors; FLT3 inhibitors; IGF-1 inhibitors; MEK inhibitors; Aurora kinase inhibitors; PKC inhibitors; RAF inhibitors; PDFGR/KIT inhibitors; VEGFR inhibitors; SRC inhibitors; retinoid receptor agonists; HDAC inhibitors; DNA methyltransferase inhibitors; and EZH2 inhibitors. 18. A method of treating bronchial premalignant lesions characterized by comprising: administering at least one of: iv. either a bronchoscopy-based procedure to examine the central airway or a chest CT scan; v. at least every 6 months, one of a bronchoscopy-based procedure to examine the central airway and a chest CT scan; and/or vi. at least one anti-inflammatory; to an individual determined to have at least one of: an increased expression level of at least one module 2 gene compared to a non-inflammatory reference level; and a reduced expression level of at least one module 6 gene compared to a non-inflammatory reference level. The method of claim 17, characterized in that at least one module 2 gene is selected from the group consisting of: MSANTD2, CCNL2 and LUC7L; and at least one of the module 6 gene is selected from the group consisting of: NEK11 and IFT88. A method according to any one of claims 17 to 18, characterized in that the subject is further determined to have an increased expression level of at least one module 7 gene, module 1 gene or module 8 gene and/or reduced expression level of at least one module 4 gene or one module 5 gene. 21. Method according to claim 19, characterized in that at least one of the module 7 gene is selected from the group consisting of: RPL26 and RPL23. 22. The method of claim 19, wherein at least one of the module 1 gene is selected from the group consisting of: KIRREL; PHLDB1; and MARVELD1. The method of claim 19, characterized in that at least one of the module 8 gene is selected from the group consisting of: DOC2; CD53; and LAPTM. 24. Method according to claim 19, characterized in that at least one of the module 4 gene is selected from the group consisting of: COX6A1 and COX7A2 25. Method according to claim 19, characterized in that at least one of the module 5 gene is selected from the group consisting of: RACGAP1 and TPX2 The method according to any one of claims 17 to 24, characterized in that the expression level of each of the genes in Table 15 is determined. The method of any one of claims 17 to 25, characterized in that at least one of the anti-inflammatory drug is selected from the group consisting of: acetylcholine receptor antagonists; acetylcholinesterase inhibitors; adenosine receptor antagonists; adrenergic receptor antagonists; angiotensin receptor antagonists; anti-IL1B antibodies; apoptosis stimulants; Aurora kinase inhibitors; CDK inhibitors; cyclooxygenase inhibitors; inhibitors of cytokine production; dopamine receptor antagonists; EGFR inhibitors; ERK1 and ERK2 phosphorylation inhibitors; estrogen receptor agonists; FLT3 inhibitors; glucocorticoid receptor agonists; glutamate receptor antagonists; HDAC inhibitors; histamine receptor antagonists; histone lysine methyltransferase inhibitors; HSP inhibitors; IKK inhibitors; ion channel antagonists; KIT inhibitors; leucine-rich repeat kinase inhibitors; MEK inhibitors; MDM inhibitors; phosphodiesterase inhibitors; monoamine oxidase inhibitors; MTOR inhibitors; NFB pathway inhibitors; nucleophosmin inhibitors; PARP inhibitors; PI3K inhibitors; PPAR receptor agonists; protein synthesis inhibitors (for example chloramphenicol); RAF inhibitors; SIRT inhibitors; sodium channel blockers; TGF beta receptor inhibitors; topoisomerase inhibitors; tyrosine kinase inhibitors; VEGFR inhibitors; and vitamin D receptor agonists. A method according to any one of claims 17 to 26, characterized in that the anti- inflammatory may be administered during a bronchoscopy-based procedure. The method of any one of claims 17 to 27, characterized in that the anti-inflammatory drug is administered systemically. A method according to any one of claims 17 to 28, characterized in that the anti-inflammatory drug is administered during a bronchoscopy-based procedure and systemically. The method according to any one of claims 1 to 29, characterized in that at least one of the gene is selected from Table 14. The method according to any one of claims 1 to 30, characterized in that the expression level of each of the genes in Table 14 is determined. Method according to any one of claims 1 to 31, characterized in that the development of lung cancer, lung squamous cell carcinoma is prevented, delayed or diminished. The method according to any one of claims 1 to 32, characterized in that the lung cancer is squamous cell carcinoma of the lung. 35. Method according to any one of claims 1 to 33, characterized in that the level of expression is the level of expression in an endobronchial biopsy, endobronchial smear sample, upper airway biopsy, upper airway smear sample, nasal epithelial cells, sputum, or blood obtained from the individual. The method of any one of claims 1 to 34, characterized in that the level of expression is the level of expression in a bronchial smear taken from the right or left main bronchus. The method of any one of claims 34 to 35, characterized in that the biopsy or smear sample comprises morphologically normal tissues or cells. The method of any one of claims 34 to 35, characterized in that the biopsy or smear sample consists of morphologically normal tissues or cells. The method of any one of claims 1 to 34, characterized in that the expression level is the expression level in a sample comprising bronchial premalignant lesion cells. 40. Method according to any one of claims 1 to 35, characterized in that the expression level is the expression level in a sample comprising morphologically normal cells. The method of any one of claims 1 to 36, characterized in that the subject is a smoker or ex-smoker.